##fileformat=VCFv4.0 ##fileDate=2015-04-16 ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 1 4430947 . CA - 2204 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.0454;PH=-0.001;PS=0.004;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.96,-225.8:3:99:64:0 1/0:-87.79,0,-68.49:1:99:57:31 1 11115197 . AGAC - 327 PASS Source=Platypus;CSQ=-|ENSG00000116649|ENST00000487300|Transcript|downstream_gene_variant||||1559|SRM|protein_coding|||||||,-|ENSG00000116649|ENST00000490101|Transcript|intron_variant&feature_truncation|||||SRM|protein_coding|||||||,-|ENSG00000116649|ENST00000376957|Transcript|intron_variant&feature_truncation|||||SRM|protein_coding|YES||||||,-|ENSG00000116649|ENST00000459997|Transcript|downstream_gene_variant||||868|SRM|nonsense_mediated_decay|||||||,-|ENSG00000116649|ENST00000465788|Transcript|downstream_gene_variant||||868|SRM|protein_coding|||||||,-|ENSG00000116649|ENST00000475189|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|62-65||||SRM|retained_intron|||||||;GR=-0.538;PH=-0.255;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-60.98,0,-65.78:0:99:44:21 0/0:0,-14.15,-168.8:1:99:51:0 1 11319967 . A G 1948 PASS Source=Platypus;CSQ=G|ENSG00000198793|ENST00000361445|Transcript|intron_variant|||||MTOR|protein_coding|YES||||||;GR=0.525;PH=0.446;PS=0.011;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/0:0,-19.57,-238:3:99:67:0 1/0:-68.25,0,-65.75:2:99:45:23 1 17627706 . GA - 498 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.472;PH=0.15;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-8.74,-159.3:5:87:50:2 1/0:-82.75,0,-52.05:5:99:39:18 1 24202810 . CCTC - 1960 PASS Source=Platypus;CSQ=-|ENSG00000188822|ENST00000536471|Transcript|intron_variant&feature_truncation|||||CNR2|protein_coding|YES||||||,-|ENSG00000188822|ENST00000374472|Transcript|intron_variant&feature_truncation|||||CNR2|protein_coding|||||||;GR=0.859;PH=0.742;PS=0.146;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-87.34,0,-78.54:2:99:55:29 1/0:-74.85,0,-64.45:2:99:49:26 1 28131087 . C T 2066 PASS Source=Platypus;CSQ=T|ENSG00000117758|ENST00000440806|Transcript|intron_variant|||||STX12|protein_coding|||||||,T|ENSG00000117758|ENST00000373943|Transcript|intron_variant|||||STX12|protein_coding|YES||||||,T|ENSG00000117758|ENST00000468761|Transcript|downstream_gene_variant||||2537|STX12|processed_transcript|||||||;GR=0.0465;PH=0.132;PS=0.147;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-168.8,-15.05,0:6:99:53:53 1/0:-38.59,0,-84.39:4:99:44:16 1 30314348 . T C 729 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.225;PH=0.257;PS=0.218;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-184.9,-15.35,0:8:99:52:52 1/1:-169.5,-13.52,0:7:99:45:45 1 33833701 . T C 2849 PASS Source=Platypus;CSQ=C|ENSG00000134686|ENST00000431992|Transcript|intron_variant|||||PHC2|protein_coding|||||||,C|ENSG00000134686|ENST00000373416|Transcript|intron_variant|||||PHC2|protein_coding|||||||,C|ENSG00000134686|ENST00000419414|Transcript|intron_variant|||||PHC2|protein_coding|||||||,C|ENSG00000233246|ENST00000432703|Transcript|downstream_gene_variant||||4855|RP11-415J8.5|antisense|YES||||||,C|ENSG00000134686|ENST00000484692|Transcript|downstream_gene_variant||||4226|PHC2|processed_transcript|||||||,C|ENSG00000134686|ENST00000468406|Transcript|downstream_gene_variant||||470|PHC2|processed_transcript|||||||,C|ENSG00000134686|ENST00000257118|Transcript|intron_variant|||||PHC2|protein_coding|YES||||||,C||ENSR00000076179|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-5.95;PH=-0.765;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-152.69,0,-169.09:1:99:112:53 0/1:-145.11,0,-129.01:0:99:91:48 1 35557607 . AC - 2444 PASS Source=Platypus;CSQ=-|ENSG00000197056|ENST00000373330|Transcript|intron_variant&feature_truncation|||||ZMYM1|protein_coding|YES||||||,-|ENSG00000197056|ENST00000373329|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZMYM1|processed_transcript|||||||,-|ENSG00000197056|ENST00000475654|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZMYM1|processed_transcript|||||||,-|ENSG00000197056|ENST00000476269|Transcript|upstream_gene_variant||||1232|ZMYM1|processed_transcript|||||||,-|ENSG00000197056|ENST00000466390|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZMYM1|processed_transcript|||||||,-|ENSG00000197056|ENST00000417119|Transcript|intron_variant&feature_truncation|||||ZMYM1|protein_coding|||||||,-|ENSG00000197056|ENST00000359858|Transcript|intron_variant&feature_truncation|||||ZMYM1|protein_coding|||||||,-|ENSG00000197056|ENST00000488455|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZMYM1|processed_transcript|||||||;GR=0.189;PH=0.25;PS=0.051;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.98,-174.8:2:99:55:1 0/1:-66.24,0,-100.64:2:99:56:23 1 39422833 . A G 2405 PASS Source=Platypus;CSQ=G|ENSG00000235549|ENST00000428233|Transcript|downstream_gene_variant||||1114|RP11-781D11.1|processed_pseudogene|YES||||||;GR=0.149;PH=0.166;PS=0.068;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-62.15,0,-79.35:3:99:48:22 0/0:0,-13.25,-159.1:2:99:45:0 1 44224344 . AA - 494 PASS Source=Platypus;CSQ=-|ENSG00000126091|ENST00000469715|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000533933|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000353126|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372366|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000532911|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000372375|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000361812|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000461066|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000533997|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000361746|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372374|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000484868|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST3GAL3|processed_transcript|||||||,-|ENSG00000126091|ENST00000372377|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372362|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000545417|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372372|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372367|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000528371|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000530581|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000372368|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000531451|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000490541|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000533212|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000372369|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000531816|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000332628|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000347631|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000351035|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000530154|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000262915|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|YES||||||,-|ENSG00000126091|ENST00000479383|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000361400|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000330208|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000372365|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000489897|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST3GAL3|nonsense_mediated_decay|||||||,-|ENSG00000126091|ENST00000531993|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000335430|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||,-|ENSG00000126091|ENST00000361392|Transcript|intron_variant&feature_truncation|||||ST3GAL3|protein_coding|||||||;GR=0.225;PH=0.257;PS=0.043;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-248.3,-20.47,0:12:99:73:73 1/1:-199.6,-16.26,0:13:99:55:55 1 49401634 . A G 2929 PASS Source=Platypus;CSQ=G|ENSG00000186094|ENST00000371839|Transcript|intron_variant|||||AGBL4|protein_coding|YES||||||,G|ENSG00000186094|ENST00000416121|Transcript|intron_variant|||||AGBL4|protein_coding|||||||,G|ENSG00000186094|ENST00000371838|Transcript|intron_variant|||||AGBL4|protein_coding|||||||,G|ENSG00000186094|ENST00000371836|Transcript|intron_variant|||||AGBL4|protein_coding|||||||;PH=0;PS=0.058;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-58.56,0,-72.76:5:99:47:22 0/0:0,-15.05,-180.9:3:99:59:0 1 49826501 . T C 1913 PASS Source=Platypus;CSQ=C|ENSG00000186094|ENST00000371839|Transcript|intron_variant|||||AGBL4|protein_coding|YES||||||,C|ENSG00000186094|ENST00000371838|Transcript|intron_variant|||||AGBL4|protein_coding|||||||,C|ENSG00000186094|ENST00000371836|Transcript|intron_variant|||||AGBL4|protein_coding|||||||;GR=0.225;PH=0.257;PS=0.037;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-9.8,-0.6,0:107:7:3:3 0/1:-10.7,0,-2.9:101:29:3:2 1 55246624 . C T 1665 PASS Source=Platypus;CSQ=T|ENSG00000006555|ENST00000371274|Transcript|downstream_gene_variant||||3600|TTC22|protein_coding|||||||,T|ENSG00000006555|ENST00000488771|Transcript|downstream_gene_variant||||645|TTC22|retained_intron|||||||,T|ENSG00000006555|ENST00000448308|Transcript|downstream_gene_variant||||3603|TTC22|protein_coding|||||||,T|ENSG00000006555|ENST00000371276|Transcript|3_prime_UTR_variant|2106||||TTC22|protein_coding|YES||||||;GR=-0.414;PH=-0.056;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:-1,-1,-1:3:99:64,62:0,0 1/2:-1,-1,-1:0:99:54,57:28,24 1 56408251 . TT - 2152 PASS Source=Platypus;CSQ=-|ENSG00000230250|ENST00000458145|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-90C4.2|lincRNA|YES||||||,-|ENSG00000233079|ENST00000455010|Transcript|upstream_gene_variant||||2508|RP11-90C4.3|lincRNA|YES||||||,-|ENSG00000227104|ENST00000426300|Transcript|upstream_gene_variant||||3298|PIGQP1|transcribed_unprocessed_pseudogene|YES||||||;PH=0.056;PS=0.168;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-229.1,-18.92,0:9:99:64:64 0/1:-68.34,0,-104.84:5:99:55:22 1 61718152 . A G 251 PASS Source=Platypus;CSQ=G|ENSG00000162599|ENST00000407417|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000162599|ENST00000371191|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000237853|ENST00000596354|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-833A20.1|lincRNA|||||||,G|ENSG00000162599|ENST00000371185|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000162599|ENST00000371184|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000162599|ENST00000371189|Transcript|intron_variant|||||NFIA|protein_coding|YES||||||,G|ENSG00000162599|ENST00000479364|Transcript|intron_variant&non_coding_transcript_variant|||||NFIA|processed_transcript|||||||,G|ENSG00000162599|ENST00000485903|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000237853|ENST00000596404|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-833A20.1|lincRNA|YES||||||,G|ENSG00000162599|ENST00000476646|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000162599|ENST00000403491|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000162599|ENST00000371187|Transcript|intron_variant|||||NFIA|protein_coding|||||||,G|ENSG00000237853|ENST00000442027|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-833A20.1|lincRNA|||||||;GR=2.2;PH=0.65;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/1:-47.37,0,-43.96:21:99:37:11 0/1:-57.4,0,-53.7:18:99:40:13 1 62681996 . T C 2412 PASS Source=Platypus;CSQ=C|ENSG00000240563|ENST00000498273|Transcript|downstream_gene_variant||||3996|L1TD1|protein_coding|YES||||||,C|ENSG00000200174|ENST00000363304|Transcript|downstream_gene_variant||||4658|Y_RNA|misc_RNA|YES||||||;GR=0.149;PH=0.166;PS=0.115;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-102.49,0,-119.89:3:99:63:30 1/0:-77.29,0,-104.89:5:99:54:22 1 66811888 . CC - 1205 PASS Source=Platypus;CSQ=-|ENSG00000184588|ENST00000341517|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000371045|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000371049|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000528771|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000526197|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000329654|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|YES||||||,-|ENSG00000184588|ENST00000531025|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||,-|ENSG00000184588|ENST00000423207|Transcript|intron_variant&feature_truncation|||||PDE4B|protein_coding|||||||;GR=-4.1;PH=-0.934;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-140.8,-12.29,0:29:99:45:45 1/1:-131.2,-10.84,0:28:99:37:37 1 67573622 . AAA - 511 PASS Source=Platypus;CSQ=-|ENSG00000203963|ENST00000475209|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||C1orf141|nonsense_mediated_decay|||||||,-|ENSG00000203963|ENST00000603691|Transcript|intron_variant&feature_truncation|||||C1orf141|protein_coding|||||||,-|ENSG00000203963|ENST00000371007|Transcript|intron_variant&feature_truncation|||||C1orf141|protein_coding|YES||||||,-|ENSG00000203963|ENST00000371004|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||C1orf141|retained_intron|||||||,-|ENSG00000203963|ENST00000448166|Transcript|intron_variant&feature_truncation|||||C1orf141|protein_coding|||||||,-|ENSG00000203963|ENST00000371006|Transcript|intron_variant&feature_truncation|||||C1orf141|protein_coding|||||||,-|ENSG00000203963|ENST00000544837|Transcript|intron_variant&feature_truncation|||||C1orf141|protein_coding|||||||;GR=-1.49;PH=-0.495;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-32.36,0,-90.26:21:99:41:12 1/0:-39.07,0,-60.67:11:99:32:13 1 68923039 . T C 1994 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-2;PH=-0.555;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.06,-190.3:3:99:59:1 0/1:-53.73,0,-81.13:16:99:49:21 1 72264330 . A G 572 PASS Source=Platypus;CSQ=G|ENSG00000172260|ENST00000467479|Transcript|intron_variant&non_coding_transcript_variant|||||NEGR1|processed_transcript|||||||,G|ENSG00000172260|ENST00000357731|Transcript|intron_variant|||||NEGR1|protein_coding|YES||||||,G|ENSG00000228853|ENST00000453121|Transcript|intron_variant&non_coding_transcript_variant|||||NEGR1-IT1|sense_intronic|YES||||||,G|ENSG00000172260|ENST00000306821|Transcript|intron_variant|||||NEGR1|protein_coding|||||||,G|ENSG00000172260|ENST00000434200|Transcript|intron_variant|||||NEGR1|protein_coding|||||||;GR=0.642;PH=0.158;PS=0.003;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-61.25,0,-75.85:3:99:47:22 1/1:-134.7,-11.44,0:1:99:39:39 1 76107237 . A G 2122 PASS Source=Platypus;CSQ=G|ENSG00000230863|ENST00000446582|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|536||||RP4-595K12.2|processed_pseudogene|YES||||||;GR=0.833;PH=0.175;PS=0.014 GT:GL:GOF:GQ:NR:NV 1/1:-136.8,-12.87,0:3:99:47:46 1/1:-130.7,-11.27,0:0:99:42:41 1 83333432 . G A 2967 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.298;PH=-1.083;PS=0.015;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-86.14,0,-102.74:22:99:66:31 0/0:0,-69.66,-189.35:3:99:52:0 1 84428431 . C T 1511 PASS Source=Platypus;CSQ=T|ENSG00000137941|ENST00000260505|Transcript|intron_variant|||||TTLL7|protein_coding|YES||||||,T|ENSG00000137941|ENST00000477524|Transcript|intron_variant&non_coding_transcript_variant|||||TTLL7|processed_transcript|||||||,T|ENSG00000137941|ENST00000474957|Transcript|intron_variant&NMD_transcript_variant|||||TTLL7|nonsense_mediated_decay|||||||,T|ENSG00000137941|ENST00000482783|Transcript|intron_variant&non_coding_transcript_variant|||||TTLL7|processed_transcript|||||||,T|ENSG00000137941|ENST00000488014|Transcript|intron_variant&non_coding_transcript_variant|||||TTLL7|processed_transcript|||||||;GR=-0.0276;PH=0.005;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-94.84,0,-80.04:11:99:60:31 0/0:0,-15.27,-192.6:1:99:55:0 1 87965198 . TT - 2876 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.02;PH=-0.539;PS=0;SD=0.949139 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.55,-159.3:2:99:51:0 0/1:-69.65,0,-66.35:1:99:49:24 1 95977610 . A G 2220 PASS Source=Platypus;CSQ=G|ENSG00000228971|ENST00000411798|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-286B14.1|lincRNA|YES||||||,G|ENSG00000228971|ENST00000440116|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-286B14.1|lincRNA|||||||,G|ENSG00000228971|ENST00000456933|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-286B14.1|lincRNA|||||||;GR=0.325;PH=0.271;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-88.98,0,-68.88:3:99:57:31 1/0:-73.76,0,-91.66:1:99:58:27 1 113152082 . GG - 1369 PASS Source=Platypus;CSQ=-|ENSG00000007341|ENST00000498383|Transcript|downstream_gene_variant||||994|ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000492274|Transcript|downstream_gene_variant||||1197|ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000459630|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000497235|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000480988|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000360743|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000361846|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST7L|nonsense_mediated_decay|||||||,-|ENSG00000007341|ENST00000497457|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000358039|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|YES||||||,-|ENSG00000007341|ENST00000369669|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000369666|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000544629|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000470683|Transcript|downstream_gene_variant||||994|ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000543570|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000463235|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000473206|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000490067|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000467335|Transcript|downstream_gene_variant||||998|ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000343210|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000479436|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000369664|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000485753|Transcript|downstream_gene_variant||||994|ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000477332|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000490715|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ST7L|nonsense_mediated_decay|||||||,-|ENSG00000007341|ENST00000466360|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||,-|ENSG00000007341|ENST00000369668|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000418497|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000538187|Transcript|intron_variant&feature_truncation|||||ST7L|protein_coding|||||||,-|ENSG00000007341|ENST00000470519|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ST7L|processed_transcript|||||||;GR=0.235;PH=0.308;PS=0.006;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-9.33,-108.6:14:93:35:0 1/0:-79.87,0,-75.37:4:99:54:27 1 117986961 . T C 675 PASS Source=Platypus;CSQ=C|ENSG00000198162|ENST00000356554|Transcript|intron_variant|||||MAN1A2|protein_coding|YES||||||,C|ENSG00000198162|ENST00000449370|Transcript|intron_variant|||||MAN1A2|protein_coding|||||||;GR=-0.0267;PH=-0.038;PS=0.077;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-185,-15.35,0:4:99:54:53 0/0:0,-10.54,-128.3:3:99:38:0 1 142781081 . TC - 2480 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.077;PS=0.035;SD=0.986408 GT:GL:GOF:GQ:NR:NV 1/1:-160.9,-19.21,0:87:99:55:54 1/1:-143.3,-20.37,0:6:99:47:46 1 150474789 . C T 2725 PASS Source=Platypus;CSQ=T|ENSG00000143374|ENST00000467982|Transcript|intron_variant&NMD_transcript_variant|||||TARS2|nonsense_mediated_decay|||||||,T|ENSG00000143374|ENST00000483046|Transcript|upstream_gene_variant||||2020|TARS2|processed_transcript|||||||,T|ENSG00000143374|ENST00000463555|Transcript|intron_variant&non_coding_transcript_variant|||||TARS2|processed_transcript|||||||,T|ENSG00000143374|ENST00000369054|Transcript|intron_variant|||||TARS2|protein_coding|||||||,T|ENSG00000143374|ENST00000438568|Transcript|downstream_gene_variant||||3078|TARS2|protein_coding|||||||,T|ENSG00000143374|ENST00000369064|Transcript|intron_variant|||||TARS2|protein_coding|YES||||||,T|ENSG00000143374|ENST00000480070|Transcript|intron_variant&non_coding_transcript_variant|||||TARS2|processed_transcript|||||||,T|ENSG00000143374|ENST00000369051|Transcript|intron_variant&NMD_transcript_variant|||||TARS2|nonsense_mediated_decay|||||||,T|ENSG00000143374|ENST00000462578|Transcript|downstream_gene_variant||||4726|TARS2|retained_intron|||||||,T|ENSG00000143374|ENST00000460794|Transcript|downstream_gene_variant||||4716|TARS2|retained_intron|||||||,T|ENSG00000143374|ENST00000606933|Transcript|intron_variant|||||TARS2|protein_coding|||||||;GR=0.158;PH=0.202;PS=0.14;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-124.53,0,-90.73:11:99:69:38 1/0:-64.57,0,-81.97:0:99:47:22 1 151152363 . ATCT - 30 PASS Source=Platypus;CSQ=-|ENSG00000163159|ENST00000491094|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||VPS72|retained_intron|||||||,-|ENSG00000163157|ENST00000601585|Transcript|upstream_gene_variant||||3603|TMOD4|processed_transcript|||||||,-|ENSG00000163157|ENST00000441701|Transcript|upstream_gene_variant||||3911|TMOD4|protein_coding|||||||,-|ENSG00000163157|ENST00000488488|Transcript|upstream_gene_variant||||3938|TMOD4|processed_transcript|||||||,-|ENSG00000163157|ENST00000463543|Transcript|upstream_gene_variant||||3906|TMOD4|nonsense_mediated_decay|||||||,-|ENSG00000163159|ENST00000496809|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||VPS72|processed_transcript|||||||,-|ENSG00000163159|ENST00000354473|Transcript|intron_variant&feature_truncation|||||VPS72|protein_coding|YES||||||,-|ENSG00000163157|ENST00000295314|Transcript|upstream_gene_variant||||3871|TMOD4|protein_coding|YES||||||,-|ENSG00000163157|ENST00000416280|Transcript|upstream_gene_variant||||3906|TMOD4|protein_coding|||||||,-|ENSG00000163159|ENST00000368892|Transcript|intron_variant&feature_truncation|||||VPS72|protein_coding|||||||;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-50.4,0,-42.7:200:99:16:12 0/1:-33.5,0,-78.96:315:99:18:7 1 172639076 . T C 696 PASS Source=Platypus;CSQ=C|ENSG00000117560|ENST00000340030|Transcript|downstream_gene_variant||||3062|FASLG|protein_coding|||||||,C|ENSG00000117560|ENST00000367721|Transcript|downstream_gene_variant||||3062|FASLG|protein_coding|YES||||||;GR=-5.02;PH=-1.141;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-108.4,0,-74.2:2:99:65:38 0/1:-83.19,0,-61.49:1:99:48:26 1 175499841 . AA - 832 PASS Source=Platypus;CSQ=-|ENSG00000116147|ENST00000367674|Transcript|intron_variant&feature_truncation|||||TNR|protein_coding|YES||||||,-|ENSG00000116147|ENST00000263525|Transcript|intron_variant&feature_truncation|||||TNR|protein_coding|||||||;GR=-3.04;PH=-0.651;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-19.51,0,-33.91:5:99:26:3 0/1:-6.09,0,-48.49:15:61:38:3 1 180972650 . A G 2702 PASS Source=Platypus;CSQ=G|ENSG00000135823|ENST00000258301|Transcript|intron_variant|||||STX6|protein_coding|YES||||||,G|ENSG00000135823|ENST00000542060|Transcript|intron_variant|||||STX6|protein_coding|||||||;GR=0.0499;PH=0;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-58.06,0,-69.16:22:99:41:19 0/0:0,-12.62,-153.7:17:99:44:0 1 184032854 . G A 170 PASS Source=Platypus;CSQ=A|ENSG00000198860|ENST00000462677|Transcript|intron_variant&NMD_transcript_variant|||||TSEN15|nonsense_mediated_decay|||||||,A|ENSG00000198860|ENST00000361641|Transcript|intron_variant|||||TSEN15|protein_coding|YES||||||,A|ENSG00000198860|ENST00000485209|Transcript|intron_variant&NMD_transcript_variant|||||TSEN15|nonsense_mediated_decay|||||||,A|ENSG00000198860|ENST00000423085|Transcript|intron_variant|||||TSEN15|protein_coding|||||||,A|ENSG00000198860|ENST00000367518|Transcript|intron_variant&non_coding_transcript_variant|||||TSEN15|retained_intron|||||||,A|ENSG00000198860|ENST00000533373|Transcript|intron_variant|||||TSEN15|protein_coding|||||||;GR=-4.68;PH=-0.759;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-82.19,0,-62.93:4:99:44:19 1/1:-165.59,-10.84,0:3:99:49:29 1 188171943 . AACC - 903 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.528;PH=-0.133;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-91.24,0,-79.64:4:99:61:32 1/0:-80.35,0,-76.65:2:99:54:26 1 189692522 . G A 1764 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=1.13;PH=0.331;PS=0.003;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-88.94,0,-80.74:15:99:58:30 0/0:0,-11.44,-147.3:3:99:40:0 1 193569904 . GA - 1413 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-2.62;PH=-0.621;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-95.25,0,-101.95:1:99:63:20 1/1:-246.3,-15.05,0:0:99:58:45 1 196504585 . ATCA - 1059 PASS Source=Platypus;CSQ=-|ENSG00000162687|ENST00000610076|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||KCNT2|processed_transcript|||||||,-|ENSG00000162687|ENST00000609185|Transcript|intron_variant&feature_truncation|||||KCNT2|protein_coding|||||||,-|ENSG00000162687|ENST00000294725|Transcript|intron_variant&feature_truncation|||||KCNT2|protein_coding|YES||||||,-|ENSG00000162687|ENST00000451324|Transcript|intron_variant&feature_truncation|||||KCNT2|protein_coding|||||||,-|ENSG00000162687|ENST00000367433|Transcript|intron_variant&feature_truncation|||||KCNT2|protein_coding|||||||,-|ENSG00000162687|ENST00000367431|Transcript|intron_variant&feature_truncation|||||KCNT2|protein_coding|||||||;GR=-1.55;PH=-0.34;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/1:-49.39,0,-40.09:4:99:39:20 0/1:-72.06,0,-36.96:5:99:41:27 1 204439600 . G A 2113 PASS Source=Platypus;CSQ=A|ENSG00000133056|ENST00000429009|Transcript|intron_variant|||||PIK3C2B|protein_coding|||||||,A|ENSG00000133056|ENST00000367187|Transcript|intron_variant|||||PIK3C2B|protein_coding|YES||||||,A|ENSG00000133056|ENST00000424712|Transcript|intron_variant|||||PIK3C2B|protein_coding|||||||,A|ENSG00000133056|ENST00000367184|Transcript|upstream_gene_variant||||3126|PIK3C2B|protein_coding|||||||,A|ENSG00000133056|ENST00000415899|Transcript|intron_variant|||||PIK3C2B|protein_coding|||||||;GR=0.301;PH=0.122;PS=0.052 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.01,-218.8:1:99:61:0 1/1:-168.9,-13.25,0:2:99:47:47 1 204668034 . C T 730 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-5.6;PH=-1.026;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-61.8,-8.84,0:7:88:56:37 0/1:-14.09,0,-12.69:13:99:31:13 1 206486450 . GCTG - 2238 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.174;PH=0.214;PS=0.998;SD=0.993851 GT:GL:GOF:GQ:NR:NV 0/1:-76.09,0,-106.39:1:99:64:27 0/0:0,-15.95,-190.3:3:99:56:0 1 220046633 . GACC - 2858 PASS Source=Platypus;CSQ=-|ENSG00000196660|ENST00000484239|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SLC30A10|processed_transcript|||||||;REPMASK=snRNA GT:GL:GOF:GQ:NR:NV 0/0:0,-17.26,-218.76:22:99:60:32 0/1:-43.28,0,-160.65:17:99:58:29 1 220379379 . G A 1194 PASS Source=Platypus;CSQ=A|ENSG00000118873|ENST00000358951|Transcript|intron_variant|||||RAB3GAP2|protein_coding|YES||||||,A|ENSG00000270585|ENST00000604232|Transcript|upstream_gene_variant||||1581|RP11-568G11.4|processed_pseudogene|YES||||||,A|ENSG00000118873|ENST00000474178|Transcript|intron_variant&NMD_transcript_variant|||||RAB3GAP2|nonsense_mediated_decay|||||||,A|ENSG00000118873|ENST00000237724|Transcript|intron_variant&non_coding_transcript_variant|||||RAB3GAP2|retained_intron|||||||,A|ENSG00000118873|ENST00000478976|Transcript|intron_variant&non_coding_transcript_variant|||||RAB3GAP2|processed_transcript|||||||,A|ENSG00000118873|ENST00000484658|Transcript|intron_variant|||||RAB3GAP2|protein_coding|||||||;GR=-3.09;PH=-0.763;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-10.48,-123.8:20:99:35:0 0/1:-40.31,0,-75.81:19:99:41:16 1 223462465 . T C 439 PASS Source=Platypus;CSQ=C|ENSG00000143502|ENST00000344029|Transcript|intron_variant|||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000608996|Transcript|intron_variant|||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000343846|Transcript|intron_variant|||||SUSD4|protein_coding|YES||||||,C|ENSG00000143502|ENST00000454695|Transcript|splice_region_variant&5_prime_UTR_variant|622||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000484758|Transcript|intron_variant|||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000494793|Transcript|intron_variant|||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000483818|Transcript|intron_variant&non_coding_transcript_variant|||||SUSD4|processed_transcript|||||||,C|ENSG00000143502|ENST00000366878|Transcript|intron_variant|||||SUSD4|protein_coding|||||||,C|ENSG00000143502|ENST00000497669|Transcript|intron_variant&non_coding_transcript_variant|||||SUSD4|processed_transcript|||||||,C|ENSG00000143502|ENST00000478605|Transcript|intron_variant&non_coding_transcript_variant|||||SUSD4|processed_transcript|||||||,C||ENSR00001529307|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.74;PH=-0.462;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-20.72,-249.9:2:99:70:0 1/0:-56.75,0,-83.85:2:99:46:20 1 226575461 . C T 723 PASS Source=Platypus;CSQ=T|ENSG00000143799|ENST00000366792|Transcript|downstream_gene_variant||||4498|PARP1|protein_coding|||||||,T|ENSG00000143799|ENST00000469663|Transcript|downstream_gene_variant||||938|PARP1|processed_transcript|||||||,T|ENSG00000143799|ENST00000366794|Transcript|intron_variant|||||PARP1|protein_coding|YES||||||;GR=0.858;PH=0.157;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-42.34,0,-29.24:2:99:35:17 0/0:0,-10.76,-126.6:2:99:40:0 1 232218290 . TCC - 601 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.109;PH=0.156;PS=0.099;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-196.7,-16.48,0:2:99:58:58 0/0:0,-13.25,-158.3:1:99:46:0 1 233445868 . A G 296 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.616;PH=0.498;PS=0.006;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-96.4,-8.1,0:3:81:32:32 1/1:-100,-8.13,0:2:81:31:30 10 2031103 . C T 1971 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.47;PH=1.135;PS=0.084 GT:GL:GOF:GQ:NR:NV 1/1:-237.4,-19.84,0:17:99:68:68 1/1:-187.5,-15.05,0:23:99:52:51 10 3021005 . T C 328 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.142;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-69.99,0,-27.19:6:99:38:26 0/0:0,-7.79,-90.3:6:78:27:0 10 3866741 . A G 2796 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-2.48;PH=-0.521;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-255.9,-20.38,0:11:99:74:72 1/1:-220.9,-18.06,0:9:99:61:61 10 5934805 . ATG - 1886 PASS Source=Platypus;CSQ=-|ENSG00000134452|ENST00000379999|Transcript|upstream_gene_variant||||1542|FBXO18|protein_coding|YES||||||,-|ENSG00000134461|ENST00000380092|Transcript|upstream_gene_variant||||2971|ANKRD16|protein_coding|||||||,-|ENSG00000134452|ENST00000462507|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FBXO18|processed_transcript|||||||,-|ENSG00000134452|ENST00000397269|Transcript|intron_variant&feature_truncation|||||FBXO18|protein_coding|||||||,-|ENSG00000134452|ENST00000470089|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FBXO18|processed_transcript|||||||,-|ENSG00000134452|ENST00000362091|Transcript|intron_variant&feature_truncation|||||FBXO18|protein_coding|||||||,-|ENSG00000134461|ENST00000380094|Transcript|upstream_gene_variant||||2944|ANKRD16|protein_coding|YES||||||,-|ENSG00000134461|ENST00000191063|Transcript|upstream_gene_variant||||2936|ANKRD16|protein_coding|||||||,-|ENSG00000134461|ENST00000492368|Transcript|upstream_gene_variant||||4872|ANKRD16|retained_intron|||||||;GR=-6.3;PH=-1.02;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-73.04,0,-101.54:1:99:57:24 0/0:0,-14.15,-176.3:0:99:48:0 10 7913512 . T C 316 PASS Source=Platypus;CSQ=C|ENSG00000165632|ENST00000344293|Transcript|intron_variant|||||TAF3|protein_coding|YES||||||;GR=0.225;PH=0.257;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-65.06,0,-57.86:1:99:44:23 0/1:-83.75,0,-71.85:3:99:52:28 10 8222816 . GG - 2980 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=3.15;PH=0.906;PS=0.045 GT:GL:GOF:GQ:NR:NV 1/1:-198.9,-16.53,0:0:99:56:56 1/1:-182.7,-14.75,0:1:99:51:51 10 8436743 . C T 495 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.451;PH=-0.945;PS=0.049;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-135.4,-10.64,0:1:99:45:42 1/1:-143.3,-12.04,0:2:99:43:42 10 14161957 . C T 2065 PASS Source=Platypus;CSQ=T|ENSG00000151474|ENST00000378503|Transcript|intron_variant|||||FRMD4A|protein_coding|||||||,T|ENSG00000151474|ENST00000493380|Transcript|intron_variant|||||FRMD4A|protein_coding|||||||,T|ENSG00000151474|ENST00000357447|Transcript|intron_variant|||||FRMD4A|protein_coding|YES||||||;GR=-0.919;PH=-0.037;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:2:46:29,29:15,15 1/1:-1,-1,-1:2:24:29,29:1,1 10 16315844 . T C 1546 PASS Source=Platypus;CSQ=C|ENSG00000226140|ENST00000417542|Transcript|upstream_gene_variant||||4856|RP11-461K13.1|lincRNA|YES||||||,C|ENSG00000226140|ENST00000434386|Transcript|upstream_gene_variant||||4856|RP11-461K13.1|lincRNA|||||||;GR=-3.92;PH=-0.856;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-179.8,-16.26,0:4:99:57:57 1/0:-63.95,0,-85.15:2:99:48:21 10 19657413 . TT - 2224 PASS Source=Platypus;CSQ=-|ENSG00000204740|ENST00000454679|Transcript|intron_variant&feature_truncation|||||MALRD1|protein_coding|||||||,-|ENSG00000204740|ENST00000441070|Transcript|intron_variant&feature_truncation|||||MALRD1|protein_coding|||||||,-|ENSG00000204740|ENST00000377266|Transcript|intron_variant&feature_truncation|||||MALRD1|protein_coding|YES||||||;GR=0.158;PH=0.175;PS=0.813;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-91.24,0,-87.74:6:99:61:29 0/0:0,-19.77,-228.4:11:99:67:0 10 24620822 rs571759456 G A 2205 PASS Source=Platypus;CSQ=A|ENSG00000120549|ENST00000430453|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A|ENSG00000120549|ENST00000376454|Transcript|intron_variant|||||KIAA1217|protein_coding|YES||||||,A|ENSG00000120549|ENST00000376456|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A|ENSG00000120549|ENST00000376452|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A|ENSG00000120549|ENST00000458595|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A|ENSG00000120549|ENST00000438429|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A|ENSG00000120549|ENST00000376462|Transcript|intron_variant|||||KIAA1217|protein_coding|||||||,A||ENSR00001421827|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.47;PH=-0.671;PS=0.011;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/1:-203.9,-12.04,0:1:99:60:38 1/1:-138.9,-8.13,0:0:81:36:25 10 26976691 . C T 2362 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.026;PH=0.001;PS=0;SD=0.921385 GT:GL:GOF:GQ:NR:NV 0/1:-52.58,0,-73.28:2:99:44:20 0/1:-73.38,0,-46.78:1:99:40:24 10 32653413 . T C 1604 PASS Source=Platypus;CSQ=C|ENSG00000229327|ENST00000417447|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-135A24.2|antisense|YES||||||,C|ENSG00000120616|ENST00000375110|Transcript|intron_variant|||||EPC1|protein_coding|||||||;GR=-0.727;PH=-0.494;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-19.49,0,-20.79:3:99:18:10 0/0:0,-4.21,-50.6:1:42:19:0 10 33891953 . G A 1869 PASS Source=Platypus;CSQ=A|ENSG00000226412|ENST00000457848|Transcript|upstream_gene_variant||||2985|RP11-476F14.1|lincRNA|YES||||||;GR=0.149;PH=0.192;PS=0.034;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-178.8,-14.45,0:5:99:51:51 1/1:-142.6,-11.71,0:2:99:42:42 10 35752891 . A G 1900 PASS Source=Platypus;CSQ=G|ENSG00000108100|ENST00000492478|Transcript|intron_variant&non_coding_transcript_variant|||||CCNY|processed_transcript|||||||,G|ENSG00000108100|ENST00000374704|Transcript|intron_variant|||||CCNY|protein_coding|YES||||||,G|ENSG00000108100|ENST00000490012|Transcript|intron_variant|||||CCNY|protein_coding|||||||,G|ENSG00000108100|ENST00000339497|Transcript|intron_variant|||||CCNY|protein_coding|||||||,G|ENSG00000108100|ENST00000374706|Transcript|intron_variant|||||CCNY|protein_coding|||||||,G|ENSG00000108100|ENST00000265375|Transcript|intron_variant|||||CCNY|protein_coding|||||||,G|ENSG00000108100|ENST00000493157|Transcript|intron_variant|||||CCNY|protein_coding|||||||,G|ENSG00000108100|ENST00000470025|Transcript|intron_variant&non_coding_transcript_variant|||||CCNY|processed_transcript|||||||,G||ENSR00000219715|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.0618;PH=0.006;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-63.86,0,-40.16:7:99:39:24 0/0:0,-7.22,-90.4:0:72:25:0 10 37482762 . ATGA - 2687 PASS Source=Platypus;CSQ=-|ENSG00000148513|ENST00000475522|Transcript|downstream_gene_variant||||626|ANKRD30A|processed_transcript|||||||,-|ENSG00000148513|ENST00000374660|Transcript|intron_variant&feature_truncation|||||ANKRD30A|protein_coding|||||||,-|ENSG00000148513|ENST00000361713|Transcript|intron_variant&feature_truncation|||||ANKRD30A|protein_coding|YES||||||,-|ENSG00000148513|ENST00000602533|Transcript|intron_variant&feature_truncation|||||ANKRD30A|protein_coding|||||||;PH=0.077;PS=0.042;SD=0.962447 GT:GL:GOF:GQ:NR:NV 1/1:-181.1,-14.75,0:1:99:51:51 1/1:-145.8,-11.74,0:0:99:40:40 10 38791173 . T C 390 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;REPMASK=Satellite GT:GL:GOF:GQ:NR:NV 0/1:-40.39,0,-2.2:14:22:22:15 0/1:-96.6,0,-4:18:40:37:34 10 44652001 . T C 1144 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.045 GT:GL:GOF:GQ:NR:NV 0/1:-7.98,0,-93.58:7:80:55:14 0/1:-1,0,-115.4:10:10:51:11 10 45892954 . AGC - 1429 PASS Source=Platypus;CSQ=-|ENSG00000012779|ENST00000374391|Transcript|intron_variant&feature_truncation|||||ALOX5|protein_coding|YES||||||,-|ENSG00000012779|ENST00000542434|Transcript|intron_variant&feature_truncation|||||ALOX5|protein_coding|||||||;GR=1.23;PH=0.831;PS=0.347;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-53.38,0,-89.38:4:99:52:22 1/0:-80.85,0,-52.05:1:99:46:27 10 48762573 . TAA - 1744 PASS Source=Platypus;CSQ=-|ENSG00000183675|ENST00000395674|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000512924|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000374235|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000505714|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPN20B|processed_transcript|||||||,-|ENSG00000183675|ENST00000507417|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000512321|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000515532|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000507697|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PTPN20B|nonsense_mediated_decay|||||||,-|ENSG00000183675|ENST00000374240|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000509230|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000395660|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000502266|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000374237|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PTPN20B|nonsense_mediated_decay|||||||,-|ENSG00000183675|ENST00000509631|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000507329|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPN20B|processed_transcript|||||||,-|ENSG00000183675|ENST00000513933|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PTPN20B|nonsense_mediated_decay|||||||,-|ENSG00000183675|ENST00000331650|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000395662|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000374233|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|YES||||||,-|ENSG00000183675|ENST00000417914|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000514592|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000510840|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000509544|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPN20B|processed_transcript|||||||,-|ENSG00000183675|ENST00000509753|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000511387|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000514491|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000504747|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPN20B|processed_transcript|||||||,-|ENSG00000183675|ENST00000395668|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||,-|ENSG00000183675|ENST00000503086|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPN20B|processed_transcript|||||||,-|ENSG00000183675|ENST00000395661|Transcript|intron_variant&feature_truncation|||||PTPN20B|protein_coding|||||||;GR=-2.45;PH=-1.666;PS=0;REPMASK=LINE;SD=0.99818 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:8:99:52,52:31,52 1/2:-1,-1,-1:6:99:46,46:25,46 10 50371310 . G A 1934 PASS Source=Platypus;CSQ=A|ENSG00000204161|ENST00000453436|Transcript|intron_variant|||||C10orf128|protein_coding|||||||,A|ENSG00000204161|ENST00000374156|Transcript|intron_variant&NMD_transcript_variant|||||C10orf128|nonsense_mediated_decay|||||||,A|ENSG00000204161|ENST00000374148|Transcript|intron_variant|||||C10orf128|protein_coding|||||||,A|ENSG00000204161|ENST00000474718|Transcript|intron_variant|||||C10orf128|protein_coding|YES||||||,A|ENSG00000204161|ENST00000374153|Transcript|intron_variant|||||C10orf128|protein_coding|||||||,A|ENSG00000204161|ENST00000488276|Transcript|intron_variant&non_coding_transcript_variant|||||C10orf128|processed_transcript|||||||,A|ENSG00000204161|ENST00000374151|Transcript|intron_variant|||||C10orf128|protein_coding|||||||,A|ENSG00000204161|ENST00000470884|Transcript|downstream_gene_variant||||3503|C10orf128|processed_transcript|||||||;GR=-0.203;PH=-0.093;PS=0.007 GT:GL:GOF:GQ:NR:NV 1/0:-35.49,0,-33.99:13:99:39:16 0/0:0,-5.72,-68.4:13:57:34:5 10 61306954 . T C 1438 PASS Source=Platypus;CSQ=C|ENSG00000235469|ENST00000446432|Transcript|downstream_gene_variant||||4208|MRPL50P4|processed_pseudogene|YES||||||;GR=-0.496;PH=-0.196;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/3:-1,-1,-1:4:99:40,40,40:19,19,19 2/2:-1,-1,-1:2:10:30,30,30:15,15,15 10 63943959 . GGT - 1994 PASS Source=Platypus;CSQ=-|ENSG00000182010|ENST00000395265|Transcript|downstream_gene_variant||||120|RTKN2|protein_coding|||||||,-|ENSG00000182010|ENST00000315289|Transcript|3_prime_UTR_variant&feature_truncation|1216-1218||||RTKN2|protein_coding|||||||,-||ENSR00001424013|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.1;PH=0.253;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.05,-183.3:1:99:53:0 1/0:-89.97,0,-65.27:1:99:49:27 10 69502588 . A G 1978 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;PH=0.056;PS=0.205;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-97.33,0,-106.73:1:99:66:32 0/0:0,-14.45,-177.8:14:99:51:0 10 73604535 . T C 802 PASS Source=Platypus;CSQ=C|ENSG00000238446|ENST00000459501|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|17||||RNU7-38P|snRNA|YES||||||,C|ENSG00000197746|ENST00000394934|Transcript|intron_variant|||||PSAP|protein_coding|||||||,C|ENSG00000197746|ENST00000394936|Transcript|intron_variant|||||PSAP|protein_coding|YES||||||;GR=0.235;PH=0.263;PS=0.033;REPMASK=snRNA GT:GL:GOF:GQ:NR:NV 1/0:-3.82,0,-8.72:22:38:52:11 0/0:0,-0.48,-5:22:6:42:14 10 75859957 . A G 743 PASS Source=Platypus;CSQ=G|ENSG00000035403|ENST00000436396|Transcript|intron_variant|||||VCL|protein_coding|||||||,G|ENSG00000035403|ENST00000478896|Transcript|intron_variant&non_coding_transcript_variant|||||VCL|processed_transcript|||||||,G|ENSG00000035403|ENST00000211998|Transcript|intron_variant|||||VCL|protein_coding|YES||||||,G|ENSG00000035403|ENST00000417648|Transcript|intron_variant|||||VCL|protein_coding|||||||,G|ENSG00000035403|ENST00000372755|Transcript|intron_variant|||||VCL|protein_coding|||||||,G|ENSG00000035403|ENST00000472585|Transcript|upstream_gene_variant||||4729|VCL|processed_transcript|||||||,G||ENSR00001424824|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.49;PH=1.293;PS=0.007 GT:GL:GOF:GQ:NR:NV 1/0:-72.37,0,-53.57:17:99:51:29 1/0:-59.76,0,-54.86:17:99:39:20 10 76580925 . C T 1752 PASS Source=Platypus;CSQ=T|ENSG00000272748|ENST00000608199|Transcript|downstream_gene_variant||||443|RP11-222G7.2|lincRNA|YES||||||,T|ENSG00000156650|ENST00000372725|Transcript|upstream_gene_variant||||4415|KAT6B|protein_coding|||||||;GR=-0.118;PH=-0.064;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-1.34,0,-42.44:13:14:21:0 1/1:-28.5,-1.47,0:17:15:16:4 10 81533521 . T C 781 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.482;PH=0.112;PS=0;SD=0.989652 GT:GL:GOF:GQ:NR:NV 1/1:-183.6,-15.33,0:24:99:52:52 0/1:-73.75,0,-73.65:12:99:55:28 10 81744753 . A G 1913 PASS Source=Platypus;CSQ=G|ENSG00000235924|ENST00000424200|Transcript|downstream_gene_variant||||2785|ZNRF2P3|processed_pseudogene|YES||||||,G|ENSG00000133661|ENST00000444384|Transcript|upstream_gene_variant||||2383|SFTPD|protein_coding|||||||,G|ENSG00000225100|ENST00000456300|Transcript|upstream_gene_variant||||1757|RP11-479O17.7|processed_pseudogene|YES||||||,G||ENSR00000358058|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;PH=0.093;PS=0.028;REPMASK=LINE;SD=0.934884 GT:GL:GOF:GQ:NR:NV 1/1:-252.8,-7.22,0:3:72:25:23 1/1:-300,-21.67,0:20:99:70:68 10 84875445 . TG - 19 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.545;PH=0.107;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-19.83,-241.5:2:99:68:0 0/1:-80.54,0,-101.94:14:99:60:28 10 85663725 . GTT - 401 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.13;PH=-0.605;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-63.99,0,-65.49:11:99:45:22 1/0:-89.35,0,-73.85:9:99:55:29 10 93904296 . T C 1414 PASS Source=Platypus;CSQ=C|ENSG00000107864|ENST00000265997|Transcript|intron_variant|||||CPEB3|protein_coding|YES||||||,C|ENSG00000107864|ENST00000412050|Transcript|intron_variant|||||CPEB3|protein_coding|||||||;GR=1.08;PH=0.735;PS=0.01;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-3.01,-36.8:2:30:11:0 0/1:-32.48,0,-27.48:1:99:21:11 10 96126007 . T C 769 PASS Source=Platypus;CSQ=C|ENSG00000173145|ENST00000461562|Transcript|upstream_gene_variant||||3291|NOC3L|processed_transcript|||||||,C|ENSG00000173145|ENST00000371361|Transcript|upstream_gene_variant||||3311|NOC3L|protein_coding|YES||||||,C|ENSG00000173145|ENST00000371350|Transcript|upstream_gene_variant||||4296|NOC3L|protein_coding|||||||,C|ENSG00000173145|ENST00000463649|Transcript|upstream_gene_variant||||3311|NOC3L|processed_transcript|||||||;GR=1.76;PH=1.071;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-68.92,0,-41.22:2:99:39:22 0/0:0,-13.85,-169.4:1:99:48:0 10 104926107 . A G 692 PASS Source=Platypus;CSQ=G|ENSG00000076685|ENST00000452156|Transcript|intron_variant&NMD_transcript_variant|||||NT5C2|nonsense_mediated_decay|||||||,G|ENSG00000076685|ENST00000369857|Transcript|intron_variant&non_coding_transcript_variant|||||NT5C2|processed_transcript|||||||,G|ENSG00000076685|ENST00000404739|Transcript|intron_variant|||||NT5C2|protein_coding|||||||,G|ENSG00000076685|ENST00000343289|Transcript|intron_variant|||||NT5C2|protein_coding|YES||||||,G|ENSG00000076685|ENST00000470299|Transcript|intron_variant|||||NT5C2|protein_coding|||||||,G|ENSG00000076685|ENST00000467380|Transcript|downstream_gene_variant||||2934|NT5C2|processed_transcript|||||||,G|ENSG00000076685|ENST00000461461|Transcript|intron_variant&NMD_transcript_variant|||||NT5C2|nonsense_mediated_decay|||||||;GR=-0.26;PH=-0.062;PS=0.417;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-80.7,-6.62,0:1:66:23:23 0/0:0,-15.65,-200.1:0:99:54:0 10 109741134 . G A 2592 PASS Source=Platypus;CSQ=A|ENSG00000229981|ENST00000598903|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000425050|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000597234|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000601410|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000593666|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000597243|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000594427|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000594566|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000601212|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||,A|ENSG00000229981|ENST00000596263|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-215N21.1|lincRNA|||||||;GR=-0.287;PH=-0.043;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 2/3:-1,-1,-1:28:99:47,39,37,40:10,7,8,0 1/4:-1,-1,-1:42:99:54,52,48,48:25,0,1,19 10 111961452 . GAT - 894 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-4.95;PH=-1.066;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-96.37,0,-65.47:2:99:56:31 0/0:0,-9.01,-110.9:2:90:31:0 10 116589791 . AGAA - 2827 PASS Source=Platypus;CSQ=-|ENSG00000151553|ENST00000369246|Transcript|intron_variant&feature_truncation|||||FAM160B1|protein_coding|||||||,-|ENSG00000151553|ENST00000369248|Transcript|intron_variant&feature_truncation|||||FAM160B1|protein_coding|YES||||||,-|ENSG00000151553|ENST00000369250|Transcript|intron_variant&feature_truncation|||||FAM160B1|protein_coding|||||||,-||ENSR00000362324|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-4.66;PH=-0.809;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-72.44,0,-104.94:109:99:65:31 0/1:-81.45,0,-71.25:123:99:55:32 10 118400133 . G A 102 PASS Source=Platypus;CSQ=A|ENSG00000165862|ENST00000298771|Transcript|intron_variant&non_coding_transcript_variant|||||PNLIPRP2|processed_transcript|||||||,A|ENSG00000165862|ENST00000433618|Transcript|intron_variant|||||PNLIPRP2|polymorphic_pseudogene|||||||,A|ENSG00000165862|ENST00000537242|Transcript|intron_variant|||||PNLIPRP2|protein_coding|YES||||||;GR=0.149;PH=0.192;PS=0.154;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-90.2,-5.48,0:11:55:67:43 0/0:0,-7.74,-79.8:17:77:56:5 10 123306415 . AA - 1439 PASS Source=Platypus;CSQ=-|ENSG00000066468|ENST00000336553|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000351936|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000346997|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000369061|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000360144|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000358487|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000369059|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000359354|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000604236|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||FGFR2|nonsense_mediated_decay|||||||,-|ENSG00000066468|ENST00000369058|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000369060|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000356226|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000357555|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000369056|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|||||||,-|ENSG00000066468|ENST00000490349|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FGFR2|processed_transcript|||||||,-|ENSG00000066468|ENST00000457416|Transcript|intron_variant&feature_truncation|||||FGFR2|protein_coding|YES||||||;GR=4.14;PH=0.82;PS=0.181 GT:GL:GOF:GQ:NR:NV 0/1:-1,-1,-1:2:30:36,50:4,5 0/2:-1,-1,-1:11:89:34,47:4,24 10 126345726 . TG - 2983 PASS Source=Platypus;CSQ=-|ENSG00000189319|ENST00000392754|Transcript|intron_variant&feature_truncation|||||FAM53B|protein_coding|||||||,-|ENSG00000189319|ENST00000337318|Transcript|intron_variant&feature_truncation|||||FAM53B|protein_coding|YES||||||,-|ENSG00000258539|ENST00000494792|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||RP11-12J10.3|nonsense_mediated_decay|YES||||||;GR=0.493;PH=0.447;PS=0.051;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 1/1:-119.7,-9.88,0:3:99:36:36 1/1:-204.5,-17.44,0:2:99:60:60 10 129239472 . ACAG - 1874 PASS Source=Platypus;CSQ=-|ENSG00000150760|ENST00000280333|Transcript|intron_variant&feature_truncation|||||DOCK1|protein_coding|YES||||||;GR=-6.49;PH=-1.905;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-6.32,-81.1:3:63:23:0 0/1:-53.45,0,-102.45:2:99:51:19 10 131102034 . G A 2326 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.358;PH=-0.128;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-40.48,-126.2:4:99:42:2 0/1:-87.37,0,-57.84:13:99:47:27 11 1412390 . C T 2878 PASS Source=Platypus;CSQ=T|ENSG00000174672|ENST00000526678|Transcript|intron_variant|||||BRSK2|protein_coding|||||||,T|ENSG00000174672|ENST00000531197|Transcript|intron_variant|||||BRSK2|protein_coding|||||||,T|ENSG00000174672|ENST00000308219|Transcript|intron_variant|||||BRSK2|protein_coding|||||||,T|ENSG00000174672|ENST00000308230|Transcript|intron_variant|||||BRSK2|protein_coding|||||||,T|ENSG00000174672|ENST00000529433|Transcript|intron_variant&NMD_transcript_variant|||||BRSK2|nonsense_mediated_decay|||||||,T|ENSG00000174672|ENST00000528841|Transcript|intron_variant|||||BRSK2|protein_coding|||||||,T||ENSR00000557091|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.37;PH=-0.062;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-14.9,-0.9,0:29:10:4:4 1/1:-13.5,-0.9,0:32:10:4:4 11 4182686 . T C 2322 PASS Source=Platypus;CSQ=C||ENSR00000317243|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=-1.29;PH=-0.51;PS=0.024 GT:GL:GOF:GQ:NR:NV 1/1:-129.8,-12.02,0:15:99:43:42 0/1:-72.5,0,-55:3:99:46:24 11 10707151 . CT - 1030 PASS Source=Platypus;CSQ=-|ENSG00000072952|ENST00000531308|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MRVI1|nonsense_mediated_decay|||||||,-|ENSG00000072952|ENST00000529068|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MRVI1|nonsense_mediated_decay|||||||,-|ENSG00000072952|ENST00000527509|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|||||||,-|ENSG00000072952|ENST00000547195|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|||||||,-|ENSG00000072952|ENST00000532037|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MRVI1|processed_transcript|||||||,-|ENSG00000072952|ENST00000529547|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|||||||,-|ENSG00000072952|ENST00000423302|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|YES||||||,-|ENSG00000072952|ENST00000531786|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MRVI1|processed_transcript|||||||,-|ENSG00000072952|ENST00000529448|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MRVI1|nonsense_mediated_decay|||||||,-|ENSG00000072952|ENST00000526414|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MRVI1|nonsense_mediated_decay|||||||,-|ENSG00000072952|ENST00000558540|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|||||||,-|ENSG00000072952|ENST00000541483|Transcript|intron_variant&feature_truncation|||||MRVI1|protein_coding|||||||;GR=0.235;PH=0.308;PS=0.411;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-7.91,-215.4:11:79:32:0 1/0:-69.25,0,-233.05:53:99:44:5 11 14168785 . G A 843 PASS Source=Platypus;CSQ=A|ENSG00000152268|ENST00000533633|Transcript|intron_variant&non_coding_transcript_variant|||||SPON1|processed_transcript|||||||,A|ENSG00000152268|ENST00000310358|Transcript|intron_variant&non_coding_transcript_variant|||||SPON1|processed_transcript|YES||||||;GR=0.149;PH=0.192;PS=0.011;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-165.7,-14.15,0:2:99:48:48 0/0:0,-14.75,-176.7:1:99:52:1 11 34464106 . C T 1144 PASS Source=Platypus;CSQ=T|ENSG00000121691|ENST00000241052|Transcript|intron_variant|||||CAT|protein_coding|YES||||||;GR=-0.674;PH=-0.44;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-185.5,-15.05,0:1:99:51:51 0/1:-95.18,0,-78.68:1:99:59:32 11 34699021 . G A 2777 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.831;PH=-0.17;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-14.39,-168:4:99:52:0 1/0:-72.75,0,-81.45:3:99:54:25 11 34811057 . C T 2138 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=4.65;PH=2.653;PS=1 GT:GL:GOF:GQ:NR:NV 1/0:-136.04,0,-54.44:4:99:66:44 0/0:0,-12.29,-147.9:3:99:43:0 11 35394993 . AA - 834 SC;MQ Source=Platypus;CSQ=-|ENSG00000110436|ENST00000449068|Transcript|intron_variant&feature_truncation|||||SLC1A2|protein_coding|||||||,-|ENSG00000110436|ENST00000606205|Transcript|intron_variant&feature_truncation|||||SLC1A2|protein_coding|||||||,-|ENSG00000110436|ENST00000395753|Transcript|intron_variant&feature_truncation|||||SLC1A2|protein_coding|||||||,-|ENSG00000110436|ENST00000395750|Transcript|intron_variant&feature_truncation|||||SLC1A2|protein_coding|||||||,-|ENSG00000215380|ENST00000357130|Transcript|upstream_gene_variant||||818|AC090625.1|processed_pseudogene|YES||||||,-|ENSG00000110436|ENST00000278379|Transcript|intron_variant&feature_truncation|||||SLC1A2|protein_coding|YES||||||;GR=-2.33;PH=-0.571;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-21.37,-264.3:2:99:71:0 0/1:-98.46,0,-86.46:1:99:60:31 11 40102160 . A G 1447 PASS Source=Platypus;CSQ=G|ENSG00000255347|ENST00000525564|Transcript|downstream_gene_variant||||3100|RP11-40H19.1|processed_pseudogene|YES||||||;GR=0.149;PH=0.166;PS=0.042;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-76.05,0,-82.55:2:99:51:24 0/0:0,-16.23,-199.1:5:99:56:0 11 40932361 . G A 264 PASS Source=Platypus;CSQ=A|ENSG00000148948|ENST00000534577|Transcript|intron_variant&non_coding_transcript_variant|||||LRRC4C|processed_transcript|||||||,A|ENSG00000148948|ENST00000528697|Transcript|intron_variant|||||LRRC4C|protein_coding|||||||,A|ENSG00000148948|ENST00000530763|Transcript|intron_variant|||||LRRC4C|protein_coding|||||||;PH=0.119;PS=0.145;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.59,-190:2:99:55:0 0/1:-85.8,0,-27.6:0:99:41:28 11 41662706 . A G 1136 PASS Source=Platypus;CSQ=G|ENSG00000255388|ENST00000531210|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-124G5.3|lincRNA|||||||,G|ENSG00000255388|ENST00000526978|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-124G5.3|lincRNA|YES||||||;PH=0.138;PS=0.031;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.85,-166.2:2:99:48:0 1/0:-64.92,0,-71.42:4:99:47:22 11 43943417 . T C 2340 PASS Source=Platypus;CSQ=C|ENSG00000244926|ENST00000528285|Transcript|upstream_gene_variant||||923|ALKBH3-AS1|antisense|||||||,C|ENSG00000166199|ENST00000529434|Transcript|downstream_gene_variant||||1601|ALKBH3|retained_intron|||||||,C|ENSG00000166199|ENST00000302708|Transcript|downstream_gene_variant||||1655|ALKBH3|protein_coding|YES||||||,C|ENSG00000166199|ENST00000532129|Transcript|downstream_gene_variant||||1601|ALKBH3|protein_coding|||||||,C|ENSG00000166199|ENST00000529366|Transcript|downstream_gene_variant||||2825|ALKBH3|protein_coding|||||||,C|ENSG00000244926|ENST00000527960|Transcript|upstream_gene_variant||||973|ALKBH3-AS1|antisense|||||||,C|ENSG00000244926|ENST00000534287|Transcript|upstream_gene_variant||||1008|ALKBH3-AS1|antisense|||||||,C|ENSG00000166199|ENST00000532962|Transcript|downstream_gene_variant||||1857|ALKBH3|nonsense_mediated_decay|||||||,C|ENSG00000166199|ENST00000530803|Transcript|downstream_gene_variant||||1601|ALKBH3|nonsense_mediated_decay|||||||,C|ENSG00000254409|ENST00000528226|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-613D13.4|sense_overlapping|||||||,C|ENSG00000166199|ENST00000532410|Transcript|downstream_gene_variant||||1694|ALKBH3|processed_transcript|||||||,C|ENSG00000254409|ENST00000526408|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-613D13.4|sense_overlapping|YES||||||,C|ENSG00000244926|ENST00000499194|Transcript|upstream_gene_variant||||941|ALKBH3-AS1|antisense|YES||||||,C|ENSG00000187479|ENST00000339446|Transcript|upstream_gene_variant||||3475|C11orf96|protein_coding|YES||||||;GR=1.49;PH=0.304;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/1:-177.9,-15.62,0:6:99:56:56 1/1:-171.8,-13.85,0:0:99:51:51 11 45459680 . T C 868 PASS Source=Platypus;CSQ=C|ENSG00000255041|ENST00000528445|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-430H10.4|lincRNA|YES||||||;GR=-2.47;PH=-0.503;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/0:-102.99,0,-94.59:1:99:59:32 0/0:0,-18.94,-227.4:1:99:65:0 11 51154929 . A G 2361 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-11.33,0,-126.53:7:99:36:5 0/1:-15.54,0,-204.64:4:99:54:1 11 58354255 . T C 404 PASS Source=Platypus;CSQ=C|ENSG00000186660|ENST00000316059|Transcript|intron_variant|||||ZFP91|protein_coding|YES||||||,C|ENSG00000255073|ENST00000389919|Transcript|intron_variant&NMD_transcript_variant|||||ZFP91-CNTF|nonsense_mediated_decay|YES||||||;GR=2.44;PH=1.382;PS=0.176 GT:GL:GOF:GQ:NR:NV 1/0:-60.13,0,-47.83:5:99:42:22 0/0:0,-12.34,-147.5:2:99:44:0 11 66893074 . C T 1841 PASS Source=Platypus;CSQ=T|ENSG00000173120|ENST00000527157|Transcript|intron_variant&non_coding_transcript_variant|||||KDM2A|processed_transcript|||||||,T|ENSG00000173120|ENST00000532436|Transcript|intron_variant&non_coding_transcript_variant|||||KDM2A|processed_transcript|||||||,T|ENSG00000173120|ENST00000398645|Transcript|intron_variant|||||KDM2A|protein_coding|||||||,T|ENSG00000173120|ENST00000529006|Transcript|intron_variant|||||KDM2A|protein_coding|YES||||||;GR=0.225;PH=0.3;PS=0.451;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-55.56,0,-58.16:2:99:50:26 1/1:-151.8,-12.87,0:2:99:50:48 11 73275410 . G A 953 PASS Source=Platypus;CSQ=A|ENSG00000054965|ENST00000450446|Transcript|intron_variant|||||FAM168A|protein_coding|||||||,A|ENSG00000054965|ENST00000356467|Transcript|intron_variant|||||FAM168A|protein_coding|YES||||||,A|ENSG00000054965|ENST00000064778|Transcript|intron_variant|||||FAM168A|protein_coding|||||||;GR=-1.24;PH=-0.377;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/1:-141.5,-12.04,0:3:99:42:42 0/1:-53.46,0,-80.86:2:99:44:19 11 74260583 . T C 1266 PASS Source=Platypus;CSQ=C|ENSG00000077514|ENST00000528481|Transcript|intron_variant|||||POLD3|protein_coding|||||||;GR=0.311;PH=0.064;PS=0.223 GT:GL:GOF:GQ:NR:NV 0/1:-104.34,0,-85.04:2:99:66:37 1/1:-157.5,-12.94,0:5:99:45:45 11 76977912 . A G 2134 PASS Source=Platypus;CSQ=G|ENSG00000178795|ENST00000527489|Transcript|downstream_gene_variant||||4489|GDPD4|processed_transcript|||||||,G|ENSG00000178795|ENST00000532155|Transcript|downstream_gene_variant||||4053|GDPD4|retained_intron|||||||,G|ENSG00000178795|ENST00000376217|Transcript|intron_variant|||||GDPD4|protein_coding|||||||,G|ENSG00000178795|ENST00000315938|Transcript|intron_variant|||||GDPD4|protein_coding|YES||||||;GR=0.225;PH=0.257;PS=0.168;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/1:-85.66,0,-81.36:2:99:50:19 0/1:-80.76,0,-111.46:1:99:54:19 11 78289632 . T C 2835 PASS Source=Platypus;CSQ=C|ENSG00000252033|ENST00000516224|Transcript|downstream_gene_variant||||668|RNU6-311P|snRNA|YES||||||,C|ENSG00000254697|ENST00000526024|Transcript|upstream_gene_variant||||3088|COPS8P3|processed_pseudogene|YES||||||,C|ENSG00000137513|ENST00000529880|Transcript|upstream_gene_variant||||4069|NARS2|protein_coding|||||||,C|ENSG00000137513|ENST00000529571|Transcript|upstream_gene_variant||||3713|NARS2|protein_coding|||||||,C|ENSG00000137513|ENST00000281038|Transcript|upstream_gene_variant||||3723|NARS2|protein_coding|YES||||||;GR=0.158;PH=0.175;PS=0.014;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-81.35,0,-71.05:0:99:54:27 0/1:-120.93,0,-93.63:0:99:72:39 11 86777190 . G A 769 PASS Source=Platypus;CSQ=A|ENSG00000166575|ENST00000305494|Transcript|intron_variant|||||TMEM135|protein_coding|YES||||||,A|ENSG00000166575|ENST00000525018|Transcript|intron_variant|||||TMEM135|protein_coding|||||||,A|ENSG00000166575|ENST00000532959|Transcript|intron_variant|||||TMEM135|protein_coding|||||||,A|ENSG00000166575|ENST00000529023|Transcript|intron_variant&non_coding_transcript_variant|||||TMEM135|retained_intron|||||||,A|ENSG00000166575|ENST00000355734|Transcript|intron_variant|||||TMEM135|protein_coding|||||||,A|ENSG00000166575|ENST00000535167|Transcript|intron_variant|||||TMEM135|protein_coding|||||||,A|ENSG00000166575|ENST00000526733|Transcript|intron_variant|||||TMEM135|protein_coding|||||||,A|ENSG00000166575|ENST00000340353|Transcript|intron_variant|||||TMEM135|protein_coding|||||||;GR=-1.13;PH=-0.257;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-49.16,0,-48.46:6:99:39:19 0/0:0,-14.85,-101.9:4:99:37:0 11 87562166 . AAG - 2392 PASS Source=Platypus;CSQ=-||ENSR00001572199|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=1.16;PH=0.824;PS=0.006;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-16.83,-201.3:1:99:57:1 0/1:-71.17,0,-94.47:1:99:56:26 11 89603627 . T C 111 PASS Source=Platypus;CSQ=C|ENSG00000189253|ENST00000329862|Transcript|3_prime_UTR_variant|1512||||TRIM64B|protein_coding|YES||||||,C|ENSG00000254558|ENST00000529293|Transcript|upstream_gene_variant||||4909|RP11-81M19.3|unprocessed_pseudogene|YES||||||;GR=1.52;PH=0.961;PS=0.001;REPMASK=Low_complexity;SD=0.996523 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.65,-185.8:5:99:54:0 1/0:-64,0,-50.6:6:99:41:23 11 111278629 . T C 679 PASS Source=Platypus;CSQ=C|ENSG00000110777|ENST00000531398|Transcript|intron_variant|||||POU2AF1|protein_coding|||||||,C|ENSG00000110777|ENST00000515029|Transcript|intron_variant&non_coding_transcript_variant|||||POU2AF1|processed_transcript|||||||,C|ENSG00000110777|ENST00000525890|Transcript|intron_variant&non_coding_transcript_variant|||||POU2AF1|processed_transcript|||||||;GR=-1.74;PH=-0.481;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-48.28,0,-61.58:13:99:50:22 0/0:0,-8.11,-97.9:2:81:34:1 11 116655326 . C T 2205 PASS Source=Platypus;CSQ=T|ENSG00000110243|ENST00000542499|Transcript|downstream_gene_variant||||4763|APOA5|protein_coding|YES||||||,T|ENSG00000110243|ENST00000227665|Transcript|downstream_gene_variant||||4757|APOA5|protein_coding|||||||,T|ENSG00000109917|ENST00000425791|Transcript|downstream_gene_variant||||1186|ZNF259|nonsense_mediated_decay|||||||,T|ENSG00000109917|ENST00000487030|Transcript|downstream_gene_variant||||2402|ZNF259|retained_intron|||||||,T|ENSG00000109917|ENST00000444935|Transcript|intron_variant|||||ZNF259|protein_coding|||||||,T|ENSG00000109917|ENST00000449430|Transcript|intron_variant&NMD_transcript_variant|||||ZNF259|nonsense_mediated_decay|||||||,T|ENSG00000109917|ENST00000498065|Transcript|downstream_gene_variant||||1915|ZNF259|retained_intron|||||||,T|ENSG00000109917|ENST00000431973|Transcript|downstream_gene_variant||||968|ZNF259|nonsense_mediated_decay|||||||,T|ENSG00000109917|ENST00000429220|Transcript|intron_variant|||||ZNF259|protein_coding|||||||,T|ENSG00000109917|ENST00000227322|Transcript|intron_variant|||||ZNF259|protein_coding|YES||||||;GR=-1.36;PH=-0.039;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.56,-188.7:1:99:53:0 0/1:-49.18,0,-84.68:0:99:44:17 11 117590949 . TTTT - 146 PASS Source=Platypus;CSQ=-|ENSG00000177103|ENST00000527706|Transcript|intron_variant&feature_truncation|||||DSCAML1|protein_coding|||||||,-|ENSG00000177103|ENST00000321322|Transcript|intron_variant&feature_truncation|||||DSCAML1|protein_coding|YES||||||;GR=2.61;PH=0.388;PS=1 GT:GL:GOF:GQ:NR:NV 0/0:0,-19.57,-243.7:2:99:66:0 0/1:-69.95,0,-80.45:1:99:48:23 11 120981491 . CA - 15 PASS Source=Platypus;CSQ=-|ENSG00000109927|ENST00000264037|Transcript|intron_variant&feature_truncation|||||TECTA|protein_coding|||||||,-|ENSG00000109927|ENST00000392793|Transcript|intron_variant&feature_truncation|||||TECTA|protein_coding|YES||||||;GR=5.79;PH=2.731;PS=0.295 GT:GL:GOF:GQ:NR:NV 1/1:-235.3,-19.87,0:2:99:68:67 1/0:-88.04,0,-80.14:1:99:55:28 11 121424703 . CCTC - 2547 PASS Source=Platypus;CSQ=-|ENSG00000137642|ENST00000524873|Transcript|upstream_gene_variant||||3018|SORL1|retained_intron|||||||,-|ENSG00000137642|ENST00000260197|Transcript|frameshift_variant&feature_truncation|2453-2456|775-776|AS/X||SORL1|protein_coding|YES||||||,-|ENSG00000137642|ENST00000529445|Transcript|upstream_gene_variant||||1045|SORL1|retained_intron|||||||,-||ENSR00001574254|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=4.86;PH=2.517;PS=0.989 GT:GL:GOF:GQ:NR:NV 1/0:-77.45,0,-62.55:7:99:52:29 0/0:0,-14.45,-172.8:18:99:48:0 11 121752126 . A G 1991 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.235;PH=0.263;PS=0.131;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-14.39,-175.6:2:99:49:0 1/1:-140.2,-11.44,0:11:99:41:41 11 122085957 . T C 1510 PASS Source=Platypus;CSQ=C|ENSG00000255090|ENST00000529804|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-820L6.1|processed_transcript|||||||,C|ENSG00000255090|ENST00000527474|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-820L6.1|lincRNA|YES||||||,C|ENSG00000255090|ENST00000529733|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-820L6.1|lincRNA|||||||,C||ENSR00000112536|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-10.2;PH=-2.104;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-88.15,0,-51.15:11:99:50:30 1/1:-151.8,-12.55,0:2:99:44:44 11 131873176 rs528117511 G A 381 PASS Source=Platypus;CSQ=A|ENSG00000182667|ENST00000374784|Transcript|intron_variant|||||NTM|protein_coding|||||||,A|ENSG00000182667|ENST00000479431|Transcript|intron_variant&non_coding_transcript_variant|||||NTM|retained_intron|||||||,A|ENSG00000182667|ENST00000498764|Transcript|intron_variant&non_coding_transcript_variant|||||NTM|processed_transcript|||||||,A|ENSG00000182667|ENST00000374791|Transcript|intron_variant|||||NTM|protein_coding|||||||,A|ENSG00000182667|ENST00000539799|Transcript|intron_variant|||||NTM|protein_coding|||||||,A|ENSG00000182667|ENST00000425719|Transcript|intron_variant|||||NTM|protein_coding|YES||||||,A|ENSG00000182667|ENST00000550167|Transcript|intron_variant|||||NTM|protein_coding|||||||,A|ENSG00000182667|ENST00000374786|Transcript|intron_variant|||||NTM|protein_coding|||||||,A|ENSG00000182667|ENST00000427481|Transcript|intron_variant|||||NTM|protein_coding|||||||;GR=0.195;PH=0.3;PS=0.318;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/0:-136.68,0,-57.88:2:99:65:44 0/0:0,-14.1,-174.8:1:99:48:0 11 134297559 . G A 2233 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.64;PH=-0.369;PS=0 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:3:99:47,47:37,37 1/0:-1,-1,-1:3:99:55,55:14,14 12 375096 . ATA - 2363 PASS Source=Platypus;CSQ=-|ENSG00000010379|ENST00000539260|Transcript|upstream_gene_variant||||3114|SLC6A13|nonsense_mediated_decay|||||||,-|ENSG00000010379|ENST00000546319|Transcript|upstream_gene_variant||||3057|SLC6A13|protein_coding|||||||,-|ENSG00000010379|ENST00000445055|Transcript|upstream_gene_variant||||3057|SLC6A13|protein_coding|||||||,-|ENSG00000010379|ENST00000536842|Transcript|upstream_gene_variant||||3094|SLC6A13|retained_intron|||||||,-|ENSG00000010379|ENST00000436453|Transcript|upstream_gene_variant||||3094|SLC6A13|protein_coding|||||||,-|ENSG00000010379|ENST00000542272|Transcript|upstream_gene_variant||||3094|SLC6A13|nonsense_mediated_decay|||||||,-|ENSG00000010379|ENST00000343164|Transcript|upstream_gene_variant||||3094|SLC6A13|protein_coding|YES||||||;GR=-0.448;PH=-0.092;PS=0.059;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-207.8,-17.16,0:3:99:58:58 1/1:-171.9,-13.85,0:0:99:47:47 12 1526042 rs146709332 A G 2454 PASS Source=Platypus;CSQ=G|ENSG00000082805|ENST00000588412|Transcript|intron_variant&NMD_transcript_variant|||||ERC1|nonsense_mediated_decay|||||||,G|ENSG00000082805|ENST00000545948|Transcript|intron_variant&NMD_transcript_variant|||||ERC1|nonsense_mediated_decay|||||||,G|ENSG00000082805|ENST00000542302|Transcript|intron_variant&NMD_transcript_variant|||||ERC1|nonsense_mediated_decay|||||||,G|ENSG00000082805|ENST00000546231|Transcript|intron_variant|||||ERC1|protein_coding|||||||,G|ENSG00000082805|ENST00000440394|Transcript|intron_variant&NMD_transcript_variant|||||ERC1|nonsense_mediated_decay|||||||,G|ENSG00000082805|ENST00000360905|Transcript|intron_variant|||||ERC1|protein_coding|||||||,G|ENSG00000082805|ENST00000347735|Transcript|intron_variant&NMD_transcript_variant|||||ERC1|nonsense_mediated_decay|||||||,G|ENSG00000082805|ENST00000589028|Transcript|intron_variant|||||ERC1|protein_coding|||||||,G|ENSG00000082805|ENST00000397203|Transcript|intron_variant|||||ERC1|protein_coding|YES||||||,G|ENSG00000082805|ENST00000543086|Transcript|intron_variant|||||ERC1|protein_coding|||||||,G|ENSG00000082805|ENST00000538971|Transcript|intron_variant&non_coding_transcript_variant|||||ERC1|retained_intron|||||||,G|ENSG00000082805|ENST00000355446|Transcript|intron_variant|||||ERC1|protein_coding|||||||,G|ENSG00000082805|ENST00000539802|Transcript|intron_variant|||||ERC1|protein_coding|||||||;GR=0.0579;PH=0.005;PS=0.034;REPMASK=SINE;UK10K=1/7562;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/1:-68.1,-7,0:2:70:26:25 1/1:-96.9,-8.64,0:2:86:36:33 12 3849462 . A G 2050 PASS Source=Platypus;CSQ=G|ENSG00000130038|ENST00000514026|Transcript|intron_variant&non_coding_transcript_variant|||||EFCAB4B|processed_transcript|||||||,G|ENSG00000130038|ENST00000535507|Transcript|intron_variant&non_coding_transcript_variant|||||EFCAB4B|processed_transcript|||||||,G|ENSG00000130038|ENST00000444507|Transcript|intron_variant|||||EFCAB4B|protein_coding|||||||,G|ENSG00000130038|ENST00000252322|Transcript|intron_variant|||||EFCAB4B|protein_coding|||||||,G|ENSG00000130038|ENST00000440314|Transcript|intron_variant|||||EFCAB4B|protein_coding|YES||||||;GR=2.25;PH=0.665;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-72.18,0,-66.98:2:99:49:23 0/0:0,-13.03,-150.2:2:99:51:2 12 6463903 . GG - 1921 PASS Source=Platypus;CSQ=-|ENSG00000111319|ENST00000541249|Transcript|downstream_gene_variant||||12|SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000539030|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000457871|Transcript|upstream_gene_variant||||188|SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000540037|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|||||||,-|ENSG00000111319|ENST00000543768|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|||||||,-|ENSG00000111319|ENST00000396966|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|||||||,-|ENSG00000111319|ENST00000228916|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|||||||,-|ENSG00000111319|ENST00000542966|Transcript|downstream_gene_variant||||599|SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000538979|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000366131|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000536087|Transcript|downstream_gene_variant||||654|SCNN1A|processed_transcript|||||||,-|ENSG00000111319|ENST00000358945|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|||||||,-|ENSG00000111319|ENST00000360168|Transcript|intron_variant&feature_truncation|||||SCNN1A|protein_coding|YES||||||,-|ENSG00000111319|ENST00000338748|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SCNN1A|nonsense_mediated_decay|||||||;GR=3.17;PH=2.009;PS=0.034 GT:GL:GOF:GQ:NR:NV 0/1:-241.84,0,-166.94:18:99:64:35 0/0:0,-18.06,-300:4:99:59:0 12 7411621 . TC - 2528 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.647;PH=0.514;PS=0.004 GT:GL:GOF:GQ:NR:NV ./.:-0.03,0,-300:38:3:70:6 1/0:-16.94,0,-300:53:99:55:9 12 8396453 . T C 2592 PASS Source=Platypus;CSQ=C|ENSG00000164845|ENST00000427893|Transcript|upstream_gene_variant||||909|FAM86FP|processed_transcript|||||||,C|ENSG00000215241|ENST00000536034|Transcript|downstream_gene_variant||||1293|RP11-266K4.9|lincRNA|||||||,C|ENSG00000215241|ENST00000304751|Transcript|downstream_gene_variant||||4911|RP11-266K4.9|lincRNA|YES||||||,C|ENSG00000164845|ENST00000338711|Transcript|upstream_gene_variant||||909|FAM86FP|transcribed_unprocessed_pseudogene|YES||||||,C||ENSR00000426016|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.379;PH=-0.461;PS=0;SD=0.966642 GT:GL:GOF:GQ:NR:NV 1/0:-1.69,0,-7.09:6:17:21:1 1/0:-2.7,0,-4.7:9:27:18:4 12 11529580 . GA - 2245 PASS Source=Platypus;CSQ=-|ENSG00000251655|ENST00000546254|Transcript|intron_variant&feature_truncation|||||PRB1|protein_coding|||||||;GR=0.641;PH=0.623;PS=0.012;SD=0.946604 GT:GL:GOF:GQ:NR:NV 1/0:-100.03,0,-95.43:1:99:67:33 1/1:-190.2,-15.65,0:2:99:53:53 12 13627002 . TTTC - 1159 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.18;PH=-0.24;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-85.26,0,-80.16:4:99:58:29 0/0:0,-18.06,-228.6:2:99:65:1 12 13665370 . CC - 522 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.13;PH=0.184;PS=0.09;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-65.34,0,-97.74:2:99:55:23 0/0:0,-15.65,-190.9:3:99:53:0 12 17351943 . T C 330 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=4.46;PH=2.236;PS=0.998 GT:GL:GOF:GQ:NR:NV 0/1:-90.92,0,-57.42:12:99:52:31 0/0:0,-13.69,-167.2:1:99:49:0 12 20683011 . T C 2029 PASS Source=Platypus;CSQ=C|ENSG00000172572|ENST00000542675|Transcript|intron_variant&non_coding_transcript_variant|||||PDE3A|retained_intron|||||||,C|ENSG00000172572|ENST00000359062|Transcript|intron_variant|||||PDE3A|protein_coding|YES||||||;GR=-0.234;PH=-0.047;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-154,-12.94,0:15:99:59:53 1/1:-106.1,-8.73,0:32:87:41:33 12 23940395 . CC - 217 PASS Source=Platypus;CSQ=-|ENSG00000134532|ENST00000309359|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000367206|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SOX5|nonsense_mediated_decay|||||||,-|ENSG00000134532|ENST00000381381|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000541847|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000546136|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000441133|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000537393|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000541536|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||,-|ENSG00000134532|ENST00000451604|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|YES||||||,-|ENSG00000134532|ENST00000545921|Transcript|intron_variant&feature_truncation|||||SOX5|protein_coding|||||||;GR=-1.18;PH=-0.08;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-82.45,0,-64.75:5:99:53:29 1/1:-142.8,-12.98,0:8:99:44:44 12 26561610 . C T 2409 PASS Source=Platypus;CSQ=T|ENSG00000123104|ENST00000538984|Transcript|downstream_gene_variant||||2536|ITPR2|retained_intron|||||||,T|ENSG00000255968|ENST00000535324|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-513G19.1|antisense|YES||||||,T|ENSG00000123104|ENST00000451599|Transcript|intron_variant&NMD_transcript_variant|||||ITPR2|nonsense_mediated_decay|||||||,T|ENSG00000123104|ENST00000381340|Transcript|intron_variant|||||ITPR2|protein_coding|YES||||||;GR=1.86;PH=0.719;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/1:-117.43,0,-81.03:3:99:71:39 0/1:-51.16,0,-69.56:3:99:41:18 12 31730053 . T C 534 PASS Source=Platypus;CSQ=C|ENSG00000170456|ENST00000544698|Transcript|intron_variant&NMD_transcript_variant|||||DENND5B|nonsense_mediated_decay|||||||,C|ENSG00000170456|ENST00000545147|Transcript|intron_variant&non_coding_transcript_variant|||||DENND5B|processed_transcript|||||||,C|ENSG00000170456|ENST00000536562|Transcript|intron_variant|||||DENND5B|protein_coding|||||||,C|ENSG00000170456|ENST00000389082|Transcript|intron_variant|||||DENND5B|protein_coding|YES||||||,C|ENSG00000170456|ENST00000354285|Transcript|intron_variant|||||DENND5B|protein_coding|||||||;GR=0.358;PH=0.084;PS=0.008 GT:GL:GOF:GQ:NR:NV 0/1:-110.77,0,-9.57:5:96:45:20 0/1:-92.72,0,-2.82:3:28:42:14 12 34093295 . G A 1053 HapScore Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=2.31;PH=0.624;PS=0.208;SD=0.952443 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:62:99:16,17:7,14 1/0:-1,-1,-1:54:10:14,14:8,10 12 38541016 . CACT - 1260 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.121;PS=0.046 GT:GL:GOF:GQ:NR:NV 1/1:-177.1,-15.3,0:4:99:54:54 1/1:-181.7,-15.87,0:2:99:54:54 12 43752356 . ATT - 725 PASS Source=Platypus;CSQ=-|ENSG00000173157|ENST00000389420|Transcript|intron_variant&feature_truncation|||||ADAMTS20|protein_coding|YES||||||;GR=0.47;PH=0.412;PS=0.006 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.32,-195:2:99:60:1 1/0:-110.04,0,-61.44:1:99:58:35 12 46741013 . A G 2022 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;PH=0.103;PS=0.029;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-170.7,-10.24,0:3:99:35:29 0/1:-112.36,0,-87.06:4:99:45:21 12 46846723 . GT - 2448 PASS Source=Platypus;CSQ=-|ENSG00000257261|ENST00000551503|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-96H19.1|lincRNA|YES||||||,-||ENSR00000429709|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=5.34;PH=2.88;PS=0.995 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.32,-146.8:3:99:61:2 0/1:-38.39,0,-52.19:4:99:47:17 12 47446790 . T C 1211 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.58;PH=1.019;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.34,-211.7:2:99:61:0 1/0:-65.39,0,-78.59:2:99:51:25 12 49260753 rs546014915 G A 1516 PASS Source=Platypus;CSQ=A|ENSG00000172602|ENST00000551243|Transcript|upstream_gene_variant||||1115|RND1|nonsense_mediated_decay|||||||,A|ENSG00000172602|ENST00000553260|Transcript|upstream_gene_variant||||4760|RND1|retained_intron|||||||,A|ENSG00000172602|ENST00000309739|Transcript|upstream_gene_variant||||1072|RND1|protein_coding|YES||||||,A||ENSR00001463297|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-3.12;PH=-1.099;PS=0;1000G=0.000599042 GT:GL:GOF:GQ:NR:NV 1/0:-72.86,0,-61.06:1:99:44:23 0/0:0,-13.85,-164.2:5:99:47:0 12 52673915 . G A 2035 PASS Source=Platypus;CSQ=A|ENSG00000170442|ENST00000423955|Transcript|intron_variant|||||KRT86|protein_coding|||||||,A|ENSG00000170442|ENST00000544024|Transcript|intron_variant|||||KRT86|protein_coding|||||||,A|ENSG00000170442|ENST00000553310|Transcript|intron_variant|||||KRT86|protein_coding|||||||,A|ENSG00000257830|ENST00000549788|Transcript|upstream_gene_variant||||975|RP11-845M18.7|antisense|YES||||||,A||ENSR00001463574|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.225;PH=0.3;PS=0.056 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:23:2:34,34,34:8,19,9 1/2:-1,-1,-1:11:3:32,32,33:8,21,12 12 55251608 . T C 1137 PASS Source=Platypus;CSQ=C|ENSG00000172551|ENST00000547958|Transcript|downstream_gene_variant||||2344|MUCL1|retained_intron|||||||,C|ENSG00000172551|ENST00000546809|Transcript|intron_variant|||||MUCL1|protein_coding|||||||,C|ENSG00000172551|ENST00000547990|Transcript|intron_variant&non_coding_transcript_variant|||||MUCL1|processed_transcript|||||||,C|ENSG00000172551|ENST00000308796|Transcript|intron_variant|||||MUCL1|protein_coding|YES||||||;GR=-2.75;PH=-0.614;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.76,-219.9:0:99:60:0 0/1:-74.64,0,-46.54:12:99:40:23 12 59826859 . C T 1865 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-1.03;PH=-0.438;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.16,-300:3:99:57:0 0/1:-126.35,0,-181.85:4:99:51:18 12 67323629 . T C 207 PASS Source=Platypus;CSQ=C|ENSG00000256248|ENST00000535721|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-123O10.4|lincRNA|YES||||||;GR=-3.46;PH=-0.893;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-186.6:3:99:53:0 1/0:-77.95,0,-68.85:16:99:50:27 12 67578929 . T C 942 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.326;PH=0.054;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-16.65,0,-121.55:83:99:47:8 1/0:-39.56,0,-109.86:114:99:48:14 12 68350024 . A G 1306 PASS Source=Platypus;CSQ=G|ENSG00000255772|ENST00000546170|Transcript|intron_variant&non_coding_transcript_variant|||||GS1-410F4.4|lincRNA|||||||;GR=-1.88;PH=-1.933;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-107.73,0,-54.83:1:99:59:37 0/0:0,-15.63,-189.1:1:99:57:0 12 70842677 . TA - 219 PASS Source=Platypus;CSQ=-|ENSG00000222405|ENST00000410473|Transcript|upstream_gene_variant||||4974|RNU4-65P|snRNA|YES||||||,-|ENSG00000268721|ENST00000600544|Transcript|upstream_gene_variant||||1312|RP11-588H23.5|processed_pseudogene|YES||||||;GR=-1.89;PH=-0.979;PS=0.005 GT:GL:GOF:GQ:NR:NV 1/1:-174.2,-14.45,0:6:99:54:52 0/1:-86.08,0,-103.78:3:99:64:29 12 78076207 . ATAT - 2041 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.944;PH=-0.499;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-164.07,-14.34,0:4:99:51:50 1/1:-203.68,-17.71,0:4:99:62:62 12 83557133 . C T 2401 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.215;PH=-0.056;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/1:-178.7,-15.6,0:2:99:60:60 1/1:-157,-13.22,0:5:99:49:49 12 85865462 . T C 880 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.496;PH=0.423;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.45,-224.9:6:99:62:0 0/1:-31.56,0,-69.26:3:99:36:12 12 86648773 . CT - 1659 PASS Source=Platypus;CSQ=-|ENSG00000182050|ENST00000602941|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MGAT4C|processed_transcript|||||||,-|ENSG00000182050|ENST00000552808|Transcript|intron_variant&feature_truncation|||||MGAT4C|protein_coding|||||||,-|ENSG00000182050|ENST00000604798|Transcript|intron_variant&feature_truncation|||||MGAT4C|protein_coding|YES||||||,-|ENSG00000182050|ENST00000552435|Transcript|intron_variant&feature_truncation|||||MGAT4C|protein_coding|||||||,-|ENSG00000182050|ENST00000549405|Transcript|intron_variant&feature_truncation|||||MGAT4C|protein_coding|||||||,-|ENSG00000182050|ENST00000551751|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MGAT4C|processed_transcript|||||||,-|ENSG00000182050|ENST00000551921|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MGAT4C|processed_transcript|||||||,-|ENSG00000182050|ENST00000547225|Transcript|intron_variant&feature_truncation|||||MGAT4C|protein_coding|||||||,-|ENSG00000182050|ENST00000550365|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MGAT4C|processed_transcript|||||||;GR=1.69;PH=0.296;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-75.79,0,-81.89:9:99:56:27 0/0:0,-13.85,-166.5:11:99:49:0 12 87032463 . T C 1551 PASS Source=Platypus;CSQ=C|ENSG00000182050|ENST00000551921|Transcript|intron_variant&non_coding_transcript_variant|||||MGAT4C|processed_transcript|||||||,C|ENSG00000258185|ENST00000550014|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-202H2.1|lincRNA|YES||||||,C|ENSG00000182050|ENST00000549405|Transcript|intron_variant|||||MGAT4C|protein_coding|||||||;GR=-1.59;PH=-0.436;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-8.71,-104:2:87:32:0 0/1:-69.85,0,-78.15:1:99:50:24 12 89531420 . G A 1798 PASS Source=Platypus;CSQ=A|ENSG00000257156|ENST00000549278|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-13A1.3|lincRNA|YES||||||;GR=-0.47;PH=-0.671;PS=0.092;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-189.5,-15.65,0:1:99:54:54 1/1:-158.3,-13.21,0:6:99:46:46 12 97487179 . T C 1974 PASS Source=Platypus;CSQ=C|ENSG00000258131|ENST00000552238|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-541G9.1|lincRNA|YES||||||;GR=-8.59;PH=-1.695;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-184.73,0,-68.73:139:99:57:55 0/1:-127.19,0,-32.99:135:99:52:41 12 100364445 . C T 419 PASS Source=Platypus;CSQ=T|ENSG00000185046|ENST00000329257|Transcript|intron_variant|||||ANKS1B|protein_coding|||||||,T|ENSG00000185046|ENST00000549866|Transcript|intron_variant|||||ANKS1B|protein_coding|||||||,T|ENSG00000185046|ENST00000547010|Transcript|intron_variant|||||ANKS1B|protein_coding|||||||,T|ENSG00000185046|ENST00000547776|Transcript|intron_variant|||||ANKS1B|protein_coding|YES||||||;GR=1.42;PH=0.302;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-102.53,0,-86.23:25:99:66:33 0/0:0,-11.74,-143.3:20:99:41:0 12 103108906 . T C 2784 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.149;PH=0.166;PS=0.197;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-32.5,0,-36.4:18:99:42:11 0/0:0,-8.51,-75.8:27:85:39:0 12 109565820 rs369171357 C T 646 PASS Source=Platypus;CSQ=T|ENSG00000076555|ENST00000539864|Transcript|upstream_gene_variant||||3343|ACACB|protein_coding|||||||,T|ENSG00000256139|ENST00000541704|Transcript|downstream_gene_variant||||2421|RP11-968O1.5|sense_overlapping|YES||||||,T|ENSG00000076555|ENST00000338432|Transcript|intron_variant|||||ACACB|protein_coding|YES||||||;GR=-0.129;PH=-0.039;PS=0.071;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-184.3,-15.32,0:2:99:55:55 1/1:-135,-11.1,0:2:99:40:39 12 111095649 . T C 172 PASS Source=Platypus;CSQ=C|ENSG00000122986|ENST00000546713|Transcript|downstream_gene_variant||||3391|HVCN1|protein_coding|||||||,C|ENSG00000122986|ENST00000547887|Transcript|intron_variant&NMD_transcript_variant|||||HVCN1|nonsense_mediated_decay|||||||,C|ENSG00000122986|ENST00000549442|Transcript|intron_variant|||||HVCN1|protein_coding|||||||,C|ENSG00000122986|ENST00000439744|Transcript|intron_variant|||||HVCN1|protein_coding|||||||,C|ENSG00000122986|ENST00000356742|Transcript|intron_variant|||||HVCN1|protein_coding|YES||||||,C|ENSG00000122986|ENST00000242607|Transcript|intron_variant|||||HVCN1|protein_coding|||||||,C|ENSG00000122986|ENST00000548312|Transcript|intron_variant|||||HVCN1|protein_coding|||||||;GR=0.212;PH=0.034;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-87.74,0,-71.74:16:99:58:30 1/0:-62.54,0,-102.74:8:99:55:21 12 113370825 . C T 2525 PASS Source=Platypus;CSQ=T|ENSG00000089127|ENST00000552526|Transcript|downstream_gene_variant||||878|OAS1|protein_coding|||||||,T|ENSG00000257452|ENST00000552784|Transcript|intron_variant&non_coding_transcript_variant|||||RP1-71H24.1|antisense|YES||||||,T|ENSG00000089127|ENST00000540589|Transcript|downstream_gene_variant||||878|OAS1|nonsense_mediated_decay|||||||,T|ENSG00000089127|ENST00000551241|Transcript|downstream_gene_variant||||835|OAS1|protein_coding|||||||;GR=0.235;PH=0.308;PS=0.032 GT:GL:GOF:GQ:NR:NV 0/1:-70.8,0,-100.5:1:99:58:25 0/0:0,-15.63,-193.7:0:99:52:0 12 114926231 . G A 2620 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.763;PH=0.19;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/0:-9.81,0,-51.01:14:98:51:8 1/0:-0.43,0,-56.92:5:6:53:9 12 119848113 . TGG - 1323 PASS Source=Platypus;CSQ=-|ENSG00000183273|ENST00000539847|Transcript|intron_variant&feature_truncation|||||CCDC60|protein_coding|||||||,-|ENSG00000183273|ENST00000536742|Transcript|intron_variant&feature_truncation|||||CCDC60|protein_coding|||||||,-|ENSG00000248636|ENST00000535511|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-768F21.1|lincRNA|||||||,-|ENSG00000248636|ENST00000509470|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-768F21.1|lincRNA|YES||||||,-|ENSG00000183273|ENST00000546345|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCDC60|processed_transcript|||||||,-|ENSG00000183273|ENST00000327554|Transcript|intron_variant&feature_truncation|||||CCDC60|protein_coding|YES||||||,-|ENSG00000248636|ENST00000537366|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-768F21.1|lincRNA|||||||,-|ENSG00000183273|ENST00000535685|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCDC60|processed_transcript|||||||;GR=-1.28;PH=-0.266;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-2.94,0,-5.34:13:29:21:4 ./.:-0.09,0,-10.79:17:3:20:4 12 121849298 . AATT - 2767 PASS Source=Platypus;CSQ=-|ENSG00000170633|ENST00000557402|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000392464|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000554868|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000361234|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000553407|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF34|retained_intron|||||||,-|ENSG00000170633|ENST00000392465|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|YES||||||,-|ENSG00000170633|ENST00000554606|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000555076|Transcript|intron_variant&feature_truncation|||||RNF34|protein_coding|||||||,-|ENSG00000170633|ENST00000556562|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF34|retained_intron|||||||;GR=-0.781;PH=-0.206;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-68.35,0,-76.75:0:99:50:24 0/1:-60.66,0,-50.16:0:99:37:20 12 126895588 . GG - 1815 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.13;PH=0.401;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-201.9,-13.52,0:11:99:47:37 1/1:-192.9,-13.2,0:11:99:52:43 12 129666006 . T C 1907 PASS Source=Platypus;CSQ=C|ENSG00000151952|ENST00000422113|Transcript|intron_variant|||||TMEM132D|protein_coding|YES||||||;GR=-0.237;PH=-0.089;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:1:99:48,51:16,32 2/2:-1,-1,-1:1:93:35,33:0,31 13 24319105 . A G 781 PASS Source=Platypus;CSQ=G|ENSG00000268735|ENST00000601943|Transcript|upstream_gene_variant||||3138|AL139080.1|protein_coding|YES||||||,G|ENSG00000027001|ENST00000464194|Transcript|intron_variant&non_coding_transcript_variant|||||MIPEP|processed_transcript|||||||,G|ENSG00000027001|ENST00000382172|Transcript|intron_variant|||||MIPEP|protein_coding|YES||||||,G|ENSG00000027001|ENST00000433710|Transcript|intron_variant|||||MIPEP|protein_coding|||||||,G||ENSR00000512942|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.03;PH=0.623;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-73.35,0,-53.55:22:99:35:10 0/0:0,-6.79,-156.6:5:68:35:0 13 24473760 . TA - 2291 PASS Source=Platypus;CSQ=-|ENSG00000205863|ENST00000382137|Transcript|upstream_gene_variant||||2566|C1QTNF9B|protein_coding|YES||||||,-|ENSG00000205863|ENST00000382057|Transcript|upstream_gene_variant||||2566|C1QTNF9B|protein_coding|||||||,-|ENSG00000205863|ENST00000382145|Transcript|upstream_gene_variant||||2119|C1QTNF9B|protein_coding|||||||,-|ENSG00000205861|ENST00000417034|Transcript|downstream_gene_variant||||2358|C1QTNF9B-AS1|antisense|||||||,-|ENSG00000205863|ENST00000382140|Transcript|intron_variant&feature_truncation|||||C1QTNF9B|protein_coding|||||||,-|ENSG00000205863|ENST00000556521|Transcript|upstream_gene_variant||||2566|C1QTNF9B|processed_transcript|||||||,-||ENSR00001507852|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.611;PH=0.17;PS=0.01;SD=0.949175 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.89,-180.8:4:99:56:0 1/0:-57.55,0,-78.25:3:99:51:22 13 35000153 . T C 53 PASS Source=Platypus;CSQ=C|ENSG00000271850|ENST00000605909|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-16D22.2|lincRNA|YES||||||;GR=-6.36;PH=-1.803;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.9,-154:2:99:45:0 1/0:-64.66,0,-37.06:6:99:39:24 13 42235132 . GC - 2935 PASS Source=Platypus;CSQ=-|ENSG00000102763|ENST00000379310|Transcript|intron_variant&feature_truncation|||||VWA8|protein_coding|YES||||||;GR=-0.934;PH=-0.622;PS=0.003;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-152.3,-13.22,0:18:99:47:46 1/1:-141,-11.44,0:15:99:42:42 13 48132257 . C T 2453 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.954;PH=0.207;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-36.97,0,-38.07:3:99:28:14 0/1:-60.66,0,-39.96:7:99:37:21 13 48373177 . T C 2777 PASS Source=Platypus;CSQ=C||ENSR00000666691|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=0.117;PH=0.029;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/0:-72.42,0,-69.22:8:99:51:26 1/0:-110.85,0,-90.35:20:99:70:39 13 49245754 rs140770019 G A 1365 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.185;PH=0.293;PS=0.005;REPMASK=LINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/1:-171.1,-14.1,0:5:99:51:51 1/1:-158,-12.64,0:1:99:44:44 13 52096610 . G A 2826 PASS Source=Platypus;CSQ=A|ENSG00000236778|ENST00000597745|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000593672|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000596050|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000595435|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000602089|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000434512|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000594959|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000599315|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000596303|Transcript|downstream_gene_variant||||4006|INTS6-AS1|antisense|||||||,A|ENSG00000236778|ENST00000601318|Transcript|intron_variant&non_coding_transcript_variant|||||INTS6-AS1|antisense|||||||;GR=0.158;PH=0.202;PS=0.072;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-67.64,0,-50.44:7:99:56:28 0/1:-60.46,0,-51.36:3:99:52:24 13 53438616 . TG - 598 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=3.32;PH=1.777;PS=0.069;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-16.13,-189.3:2:99:58:0 1/0:-91.96,0,-87.46:6:99:60:31 13 61947637 . C T 281 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.235;PH=0.308;PS=0.041;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-130.1,-11.14,0:2:99:40:40 1/0:-74.96,0,-49.66:1:99:42:25 13 66547826 . A G 828 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.266;PH=0.33;PS=0.858;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-235.19,0,-113.39:5:99:58:37 0/0:0,-15.05,-300:2:99:51:0 13 66584477 . GATG - 2149 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.064;PS=0.12;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-74.57,0,-82.97:2:99:57:27 0/0:0,-14.72,-175.3:4:99:52:0 13 72568769 . A G 551 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-2.37;PH=-0.471;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-26.68,0,-44.58:15:99:25:8 0/0:0,-5.43,-126.9:23:54:40:5 13 73003667 . CA - 206 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.36;PH=0.331;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-170.1,-14.45,0:2:99:49:49 1/0:-74.85,0,-61.15:7:99:47:25 13 77821169 . T C 1399 PASS Source=Platypus;CSQ=C|ENSG00000005810|ENST00000357337|Transcript|intron_variant|||||MYCBP2|protein_coding|||||||,C|ENSG00000005810|ENST00000544440|Transcript|intron_variant|||||MYCBP2|protein_coding|YES||||||,C|ENSG00000005810|ENST00000360084|Transcript|intron_variant|||||MYCBP2|protein_coding|||||||,C|ENSG00000005810|ENST00000407578|Transcript|intron_variant|||||MYCBP2|protein_coding|||||||;GR=0.0673;PH=0.026;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.15,-169.7:9:99:50:0 0/1:-72.5,0,-84.7:5:99:55:26 13 78818266 . CTT - 834 PASS Source=Platypus;CSQ=-|ENSG00000234377|ENST00000430549|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000606124|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000606803|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000607862|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|YES||||||,-|ENSG00000234377|ENST00000607205|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000606187|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000607220|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000605996|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000560209|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000606376|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000444769|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000606429|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||,-|ENSG00000234377|ENST00000607860|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RNF219-AS1|antisense|||||||;GR=-0.215;PH=-0.076;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-44.87,0,-71.37:3:99:44:17 1/0:-45.05,0,-89.05:2:99:49:17 13 82201068 . C T 2079 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.43;PH=0.265;PS=0.046 GT:GL:GOF:GQ:NR:NV 1/1:-108.1,-9.26,0:2:93:34:34 1/1:-127.7,-10.24,0:2:99:35:35 13 88055534 . G A 948 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.47;PH=-0.666;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.12,-167.4:4:99:50:0 1/1:-177.9,-15.05,0:2:99:55:54 13 90285816 . CAG - 2151 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-2.59;PH=-0.831;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-18.64,-219.6:4:99:66:0 1/0:-67.73,0,-59.63:3:99:45:24 13 92796233 . T C 2909 PASS Source=Platypus;CSQ=C|ENSG00000179399|ENST00000377067|Transcript|intron_variant|||||GPC5|protein_coding|YES||||||;GR=-1.53;PH=-0.091;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-62.26,0,-46.86:15:99:37:20 1/1:-144.4,-12.01,0:32:99:42:42 13 95292558 . T C 2933 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-1.08;PH=-0.183;PS=0.004 GT:GL:GOF:GQ:NR:NV 0/1:-87.73,0,-123.43:3:99:69:29 0/1:-55.98,0,-84.18:1:99:45:19 13 97356941 . GG - 1666 PASS Source=Platypus;CSQ=-|ENSG00000185352|ENST00000376705|Transcript|intron_variant&feature_truncation|||||HS6ST3|protein_coding|YES||||||;GR=-0.0345;PH=-0.05;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-201.4,-16.86,0:7:99:59:59 1/0:-122.03,0,-81.43:7:99:66:39 13 98760792 . A G 1715 PASS Source=Platypus;CSQ=G||ENSR00001511641|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,G||||intergenic_variant|||||||||||||;GR=0.0145;PH=-0.034;PS=0.02;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-73.13,0,-253.73:2:99:55:8 1/0:-93.01,0,-246.61:2:99:45:9 13 104480522 . C T 2929 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.064;PS=0.358;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-78.25,0,-64.95:2:99:51:28 0/0:0,-16.02,-190:3:99:55:0 13 105236395 . A G 1666 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-3.17;PH=-0.623;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-38.71,0,-48.31:20:99:42:12 0/0:0,-10.84,-132.4:1:99:52:0 13 107130719 . A G 2337 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-0.294;PH=-0.036;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-99.2,-8.73,0:10:87:34:33 1/1:-179,-15.6,0:7:99:55:54 13 109059883 . T C 2631 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.73;PH=-0.135;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-184.4,-15.35,0:3:99:53:53 1/1:-183.7,-15.05,0:0:99:52:52 13 110161725 . C T 2965 PASS Source=Platypus;CSQ=T||ENSR00001512235|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,T||||intergenic_variant|||||||||||||;GR=-1.35;PH=-0.426;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-211.3,-18.34,0:45:99:62:62 1/1:-176,-14.67,0:53:99:52:52 13 111291196 . C T 909 PASS Source=Platypus;CSQ=T|ENSG00000134905|ENST00000541239|Transcript|downstream_gene_variant||||2563|CARS2|retained_intron|||||||,T|ENSG00000134905|ENST00000481787|Transcript|downstream_gene_variant||||2594|CARS2|retained_intron|||||||,T|ENSG00000213995|ENST00000397191|Transcript|downstream_gene_variant||||3320|CARKD|protein_coding|||||||,T|ENSG00000213995|ENST00000424185|Transcript|3_prime_UTR_variant|1052||||CARKD|protein_coding|||||||,T|ENSG00000134905|ENST00000537802|Transcript|downstream_gene_variant||||2570|CARS2|retained_intron|||||||,T|ENSG00000134905|ENST00000540006|Transcript|downstream_gene_variant||||2563|CARS2|retained_intron|||||||,T|ENSG00000213995|ENST00000309957|Transcript|3_prime_UTR_variant|1515||||CARKD|protein_coding|YES||||||,T|ENSG00000255831|ENST00000545740|Transcript|upstream_gene_variant||||359|AL139385.1|pseudogene|YES||||||,T|ENSG00000213995|ENST00000458711|Transcript|3_prime_UTR_variant|984||||CARKD|protein_coding|||||||,T|ENSG00000213995|ENST00000470164|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|1233||||CARKD|processed_transcript|||||||,T|ENSG00000134905|ENST00000480437|Transcript|downstream_gene_variant||||3598|CARS2|processed_transcript|||||||,T|ENSG00000134905|ENST00000535516|Transcript|downstream_gene_variant||||2570|CARS2|retained_intron|||||||,T|ENSG00000134905|ENST00000471986|Transcript|downstream_gene_variant||||3538|CARS2|processed_transcript|||||||,T|ENSG00000134905|ENST00000487253|Transcript|downstream_gene_variant||||2738|CARS2|nonsense_mediated_decay|||||||,T|ENSG00000134905|ENST00000257347|Transcript|downstream_gene_variant||||2568|CARS2|protein_coding|YES||||||,T|ENSG00000134905|ENST00000542774|Transcript|downstream_gene_variant||||2735|CARS2|processed_transcript|||||||,T|ENSG00000134905|ENST00000535615|Transcript|downstream_gene_variant||||3662|CARS2|retained_intron|||||||,T|ENSG00000134905|ENST00000375781|Transcript|downstream_gene_variant||||2568|CARS2|retained_intron|||||||;GR=-0.934;PH=-0.732;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-70.97,0,-82.77:2:99:53:25 0/1:-81.28,0,-97.08:2:99:61:28 13 111314197 . AC - 1017 PASS Source=Platypus;CSQ=-|ENSG00000134905|ENST00000537743|Transcript|downstream_gene_variant||||987|CARS2|protein_coding|||||||,-|ENSG00000134905|ENST00000535398|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|processed_transcript|||||||,-|ENSG00000134905|ENST00000535516|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000481787|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000543487|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|processed_transcript|||||||,-|ENSG00000134905|ENST00000539405|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000537386|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000487253|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CARS2|nonsense_mediated_decay|||||||,-|ENSG00000134905|ENST00000257347|Transcript|intron_variant&feature_truncation|||||CARS2|protein_coding|YES||||||,-|ENSG00000134905|ENST00000537802|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000535615|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000540006|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000541362|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000545506|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||,-|ENSG00000134905|ENST00000375781|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CARS2|retained_intron|||||||;GR=0.354;PH=0.338;PS=0.024;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-14.45,-177.7:4:99:51:0 0/1:-96.4,0,-81.3:16:99:61:34 13 111663795 . G A 1309 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=1.31;PH=1.066;PS=0.306 GT:GL:GOF:GQ:NR:NV 0/0:0,-6.92,-135.4:1:69:26:0 0/1:-82.66,0,-118.96:1:99:45:14 13 112061950 . AA - 2761 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.102;PH=0.015;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.49,-155.4:3:99:49:0 1/0:-61.56,0,-56.66:1:99:43:23 13 112270438 . GT - 2102 PASS Source=Platypus;CSQ=-|ENSG00000215881|ENST00000401043|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-65D24.1|sense_overlapping|YES||||||,-|ENSG00000204398|ENST00000375713|Transcript|intron_variant&feature_truncation|||||RP11-65D24.2|protein_coding|YES||||||;GR=1.11;PH=0.879;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-298.3,0,-298.3:346:99:220:0 0/1:-276.85,0,-298.3:313:99:179:0 13 113138444 . TAA - 1204 PASS Source=Platypus;CSQ=-|ENSG00000126216|ENST00000261965|Transcript|downstream_gene_variant||||879|TUBGCP3|protein_coding|YES||||||,-|ENSG00000126216|ENST00000469302|Transcript|downstream_gene_variant||||1712|TUBGCP3|processed_transcript|||||||;GR=-2.13;PH=-0.556;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-231.71,0,-298.49:3:99:72:15 0/1:-76.01,0,-298.49:4:99:56:5 14 19400894 . A G 1123 PASS Source=Platypus;CSQ=G|ENSG00000258233|ENST00000548856|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|2371||||ARHGAP42P5|processed_pseudogene|YES||||||;PH=0.103;PS=0.022;SD=0.996027 GT:GL:GOF:GQ:NR:NV 1/0:-54.95,0,-82.05:2:99:45:18 1/1:-124.1,-10.17,0:40:99:33:33 14 19763699 . G A 1093 PASS Source=Platypus;CSQ=A|ENSG00000258781|ENST00000547821|Transcript|downstream_gene_variant||||4917|RP11-496I2.4|unprocessed_pseudogene|YES||||||;PH=0.064;PS=0.125;REPMASK=LINE;SD=0.994191 GT:GL:GOF:GQ:NR:NV 0/1:-35.87,0,-58.47:4:99:38:16 0/1:-45.56,0,-70.06:1:99:43:17 14 20794390 . GTGT - 2871 PASS Source=Platypus;CSQ=-|ENSG00000100814|ENST00000555963|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNB1IP1|processed_transcript|||||||,-|ENSG00000222489|ENST00000410557|Transcript|upstream_gene_variant||||2905|SNORA79|snoRNA|YES||||||,-|ENSG00000100814|ENST00000398169|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|YES||||||,-|ENSG00000100814|ENST00000556854|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CCNB1IP1|nonsense_mediated_decay|||||||,-|ENSG00000100814|ENST00000556563|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000353689|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000557114|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNB1IP1|processed_transcript|||||||,-|ENSG00000100814|ENST00000358932|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000553291|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000553516|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNB1IP1|processed_transcript|||||||,-|ENSG00000100814|ENST00000557665|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000398163|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000398160|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000238344|ENST00000459475|Transcript|downstream_gene_variant||||216|SNORD126|snoRNA|YES||||||,-|ENSG00000100814|ENST00000437553|Transcript|intron_variant&feature_truncation|||||CCNB1IP1|protein_coding|||||||,-|ENSG00000100814|ENST00000555348|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNB1IP1|processed_transcript|||||||,-||ENSR00000414851|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.653;PH=0.052;PS=0.01 GT:GL:GOF:GQ:NR:NV 0/2:-1,-1,-1:22:24:50,50:29,29 1/2:-1,-1,-1:14:17:51,51:24,24 14 22655298 . A G 729 PASS Source=Platypus;CSQ=G|ENSG00000258905|ENST00000553993|Transcript|downstream_gene_variant||||1345|TRAV32|TR_V_pseudogene|YES||||||,G|ENSG00000258812|ENST00000557514|Transcript|upstream_gene_variant||||2754|TRAV33|TR_V_pseudogene|YES||||||;GR=0.514;PH=0.426;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-27.92,0,-19.62:3:99:18:9 0/1:-17.76,0,-28.16:6:99:20:7 14 23269806 . CAAC - 695 HapScore Source=Platypus;CSQ=-|ENSG00000155465|ENST00000397528|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|||||||,-|ENSG00000155465|ENST00000397529|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|||||||,-|ENSG00000155465|ENST00000285850|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|||||||,-|ENSG00000155465|ENST00000556287|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SLC7A7|nonsense_mediated_decay|||||||,-|ENSG00000155465|ENST00000397532|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|YES||||||,-|ENSG00000155465|ENST00000555702|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|||||||,-|ENSG00000155465|ENST00000554517|Transcript|intron_variant&feature_truncation|||||SLC7A7|protein_coding|||||||;GR=0.894;PH=0.799;PS=0.018;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-15.89,-189.1:10:99:55:0 0/1:-80.94,0,-110.34:5:99:64:27 14 25558927 . C T 2117 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-1.06;PH=-1.767;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-58.15,0,-94.85:1:99:52:21 1/0:-77.87,0,-77.27:2:99:53:26 14 27182743 . A G 2521 PASS Source=Platypus;CSQ=G|ENSG00000257842|ENST00000552826|Transcript|intron_variant&non_coding_transcript_variant|||||NOVA1-AS1|antisense|||||||;GR=-4.45;PH=-0.971;PS=0;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 1/1:-186.3,-15.89,0:7:99:55:55 1/1:-178.8,-14.43,0:3:99:49:49 14 27972616 . TACG - 652 PASS Source=Platypus;CSQ=-|ENSG00000258932|ENST00000555797|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTD-3006G17.2|processed_transcript|||||||,-|ENSG00000258932|ENST00000554904|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTD-3006G17.2|processed_transcript|||||||,-|ENSG00000258932|ENST00000556890|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTD-3006G17.2|processed_transcript|||||||,-|ENSG00000258932|ENST00000553392|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTD-3006G17.2|processed_transcript|YES||||||;GR=0.149;PH=0.166;PS=0.02;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-82.05,0,-79.55:0:99:51:26 0/1:-131.56,0,-79.56:1:99:68:40 14 30158304 . CCAA - 2199 PASS Source=Platypus;CSQ=-|ENSG00000184304|ENST00000415220|Transcript|intron_variant&feature_truncation|||||PRKD1|protein_coding|||||||,-|ENSG00000184304|ENST00000331968|Transcript|intron_variant&feature_truncation|||||PRKD1|protein_coding|YES||||||,-|ENSG00000184304|ENST00000549503|Transcript|intron_variant&feature_truncation|||||PRKD1|protein_coding|||||||;GR=0.235;PH=0.308;PS=0.192;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.85,-164.3:2:99:48:0 1/0:-72.95,0,-65.25:4:99:46:24 14 32599538 . C T 1492 PASS Source=Platypus;CSQ=T|ENSG00000100852|ENST00000554090|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000539826|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000432921|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000396582|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000433497|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000345122|Transcript|intron_variant|||||ARHGAP5|protein_coding|YES||||||,T|ENSG00000100852|ENST00000556611|Transcript|intron_variant|||||ARHGAP5|protein_coding|||||||,T|ENSG00000100852|ENST00000557643|Transcript|intron_variant&NMD_transcript_variant|||||ARHGAP5|nonsense_mediated_decay|||||||;GR=-0.334;PH=-0.782;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-69.27,0,-57.27:3:99:43:23 0/0:0,-12.01,-142.2:3:99:42:0 14 33243895 . T C 176 PASS Source=Platypus;CSQ=C|ENSG00000151320|ENST00000554740|Transcript|downstream_gene_variant||||688|AKAP6|protein_coding|||||||,C|ENSG00000151320|ENST00000280979|Transcript|intron_variant|||||AKAP6|protein_coding|YES||||||,C|ENSG00000151320|ENST00000556540|Transcript|downstream_gene_variant||||860|AKAP6|processed_transcript|||||||,C|ENSG00000151320|ENST00000555207|Transcript|downstream_gene_variant||||898|AKAP6|processed_transcript|||||||,C|ENSG00000151320|ENST00000557272|Transcript|intron_variant|||||AKAP6|protein_coding|||||||;GR=0.681;PH=0.37;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.84,-201.9:2:99:58:0 0/1:-74.56,0,-58.96:1:99:43:24 14 36596099 . T C 2499 PASS Source=Platypus;CSQ=C|ENSG00000257585|ENST00000546508|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00609|lincRNA|YES||||||;GR=0.903;PH=0.06;PS=0.089 GT:GL:GOF:GQ:NR:NV 1/0:-63.1,0,-118.3:3:99:65:25 1/0:-78.62,0,-80.22:2:99:62:33 14 36721265 . GA - 2764 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.633;PH=-0.27;PS=0.031;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-7.83,-70.9:5:78:59:3 0/1:-14.77,0,-12.67:1:99:35:13 14 37706264 . T C 858 PASS Source=Platypus;CSQ=C|ENSG00000151338|ENST00000555870|Transcript|intron_variant&NMD_transcript_variant|||||MIPOL1|nonsense_mediated_decay|||||||,C|ENSG00000151338|ENST00000556451|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000536774|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000327441|Transcript|intron_variant|||||MIPOL1|protein_coding|YES||||||,C|ENSG00000151338|ENST00000537471|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000396294|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000556753|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000545536|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000556615|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||,C|ENSG00000151338|ENST00000554114|Transcript|upstream_gene_variant||||3365|MIPOL1|processed_transcript|||||||,C|ENSG00000151338|ENST00000554930|Transcript|intron_variant&non_coding_transcript_variant|||||MIPOL1|processed_transcript|||||||,C|ENSG00000151338|ENST00000539062|Transcript|intron_variant|||||MIPOL1|protein_coding|||||||;GR=0.662;PH=0.544;PS=0.007;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.4,-171.2:8:99:49:0 1/1:-168.6,-14.12,0:1:99:49:49 14 42208252 . GA - 337 PASS Source=Platypus;CSQ=-|ENSG00000165379|ENST00000555279|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LRFN5|processed_transcript|||||||,-|ENSG00000165379|ENST00000298119|Transcript|intron_variant&feature_truncation|||||LRFN5|protein_coding|YES||||||,-|ENSG00000258536|ENST00000553366|Transcript|upstream_gene_variant||||3589|RP11-1053O12.1|processed_pseudogene|YES||||||,-|ENSG00000165379|ENST00000554120|Transcript|intron_variant&feature_truncation|||||LRFN5|protein_coding|||||||,-|ENSG00000165379|ENST00000554171|Transcript|intron_variant&feature_truncation|||||LRFN5|protein_coding|||||||;GR=0.131;PH=0.171;PS=0.037;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-69.71,0,-61.89:6:99:48:23 0/0:0,-9.33,-105.22:7:93:35:0 14 45500161 . A G 835 PASS Source=Platypus;CSQ=G|ENSG00000198718|ENST00000556105|Transcript|downstream_gene_variant||||2662|FAM179B|retained_intron|||||||,G|ENSG00000179454|ENST00000556239|Transcript|intron_variant|||||KLHL28|protein_coding|||||||,G|ENSG00000198718|ENST00000555586|Transcript|downstream_gene_variant||||3624|FAM179B|retained_intron|||||||,G|ENSG00000198718|ENST00000557423|Transcript|intron_variant&NMD_transcript_variant|||||FAM179B|nonsense_mediated_decay|||||||,G|ENSG00000198718|ENST00000361577|Transcript|intron_variant|||||FAM179B|protein_coding|YES||||||,G|ENSG00000198718|ENST00000382233|Transcript|intron_variant|||||FAM179B|protein_coding|||||||,G|ENSG00000179454|ENST00000553817|Transcript|intron_variant&non_coding_transcript_variant|||||KLHL28|processed_transcript|||||||,G|ENSG00000198718|ENST00000361462|Transcript|intron_variant|||||FAM179B|protein_coding|||||||;GR=1.44;PH=0.907;PS=0.242;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-9.9,0,-19.32:62:99:16:3 0/1:-26.9,0,-34.74:47:99:28:10 14 49164580 . A G 629 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.225;PH=0.257;PS=0.129;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-66.45,0,-76.95:1:99:50:23 1/0:-83.45,0,-67.05:6:99:48:25 14 49391412 . C T 332 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.71;PH=0.667;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/1:-213,-17.16,0:2:99:60:59 0/1:-61.25,0,-91.55:3:99:51:22 14 50831430 . C T 390 PASS Source=Platypus;CSQ=T|ENSG00000100490|ENST00000528197|Transcript|upstream_gene_variant||||736|CDKL1|processed_transcript|||||||,T|ENSG00000100490|ENST00000356146|Transcript|intron_variant&non_coding_transcript_variant|||||CDKL1|processed_transcript|||||||,T|ENSG00000100490|ENST00000531052|Transcript|intron_variant&non_coding_transcript_variant|||||CDKL1|processed_transcript|||||||,T|ENSG00000100490|ENST00000216378|Transcript|intron_variant|||||CDKL1|protein_coding|||||||,T|ENSG00000100490|ENST00000395834|Transcript|intron_variant|||||CDKL1|protein_coding|YES||||||;GR=1.1;PH=0.385;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-0.54,-100.71:8:7:28:9 1/0:-2.57,0,-96.14:8:26:26:11 14 51097162 . C T 2675 PASS Source=Platypus;CSQ=T|ENSG00000198513|ENST00000556067|Transcript|intron_variant&NMD_transcript_variant|||||ATL1|nonsense_mediated_decay|||||||,T|ENSG00000198513|ENST00000354525|Transcript|intron_variant|||||ATL1|protein_coding|||||||,T|ENSG00000151748|ENST00000553731|Transcript|downstream_gene_variant||||4384|SAV1|protein_coding|||||||,T|ENSG00000151748|ENST00000555720|Transcript|downstream_gene_variant||||1614|SAV1|protein_coding|||||||,T|ENSG00000198513|ENST00000555266|Transcript|downstream_gene_variant||||2293|ATL1|nonsense_mediated_decay|||||||,T|ENSG00000198513|ENST00000357032|Transcript|intron_variant|||||ATL1|protein_coding|||||||,T|ENSG00000198513|ENST00000358385|Transcript|intron_variant|||||ATL1|protein_coding|YES||||||,T|ENSG00000151748|ENST00000324679|Transcript|downstream_gene_variant||||3192|SAV1|protein_coding|YES||||||,T|ENSG00000198513|ENST00000441560|Transcript|intron_variant|||||ATL1|protein_coding|||||||,T|ENSG00000151748|ENST00000557458|Transcript|downstream_gene_variant||||4669|SAV1|protein_coding|||||||;GR=1.41;PH=0.221;PS=0.023 GT:GL:GOF:GQ:NR:NV 1/0:-1,-1,-1:6:17:20,20:3,3 0/2:-1,-1,-1:7:18:19,19:4,4 14 53483364 . GA - 892 PASS Source=Platypus;CSQ=-|ENSG00000258503|ENST00000554238|Transcript|downstream_gene_variant||||4379|RP11-368P15.1|processed_pseudogene|YES||||||,-||ENSR00000417847|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.149;PH=0.192;PS=0.25;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-11.25,0,-106.95:3:99:41:10 0/1:-16.46,0,-90.16:9:99:36:11 14 58855478 . TA - 2003 PASS Source=Platypus;CSQ=-|ENSG00000258658|ENST00000556390|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-517O13.3|antisense|YES||||||;PH=0.103;PS=0.659;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-102.2,-8.7,0:3:87:31:31 0/0:0,-13.25,-163.1:10:99:47:0 14 62577601 . T C 2201 PASS Source=Platypus;CSQ=C|ENSG00000258403|ENST00000553426|Transcript|upstream_gene_variant||||3470|RP11-355I22.6|lincRNA|YES||||||,C|ENSG00000259796|ENST00000568344|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|9||||RP11-355I22.7|sense_overlapping|YES||||||,C|ENSG00000258903|ENST00000554252|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-355I22.2|lincRNA|YES||||||;GR=-3;PH=-0.643;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-215,-17.46,0:1:99:59:59 1/1:-161.4,-13.25,0:2:99:46:46 14 62698736 . TGC - 2083 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.131;PH=0.148;PS=0.05;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-92.24,0,-72.24:3:99:58:31 1/0:-104.84,0,-69.34:0:99:57:34 14 63377194 . A G 2356 PASS Source=Platypus;CSQ=G|ENSG00000140015|ENST00000394968|Transcript|intron_variant|||||KCNH5|protein_coding|||||||,G|ENSG00000140015|ENST00000322893|Transcript|intron_variant|||||KCNH5|protein_coding|YES||||||,G|ENSG00000140015|ENST00000420622|Transcript|intron_variant|||||KCNH5|protein_coding|||||||;GR=2.01;PH=1.175;PS=0.322;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-110.54,0,-72.74:0:99:60:34 0/0:0,-13.55,-167.1:1:99:46:0 14 64530615 . CTC - 1771 PASS Source=Platypus;CSQ=-|ENSG00000054654|ENST00000554584|Transcript|intron_variant&feature_truncation|||||SYNE2|protein_coding|||||||,-|ENSG00000054654|ENST00000357395|Transcript|intron_variant&feature_truncation|||||SYNE2|protein_coding|||||||,-|ENSG00000054654|ENST00000358025|Transcript|intron_variant&feature_truncation|||||SYNE2|protein_coding|YES||||||,-|ENSG00000054654|ENST00000555002|Transcript|intron_variant&feature_truncation|||||SYNE2|protein_coding|||||||,-|ENSG00000054654|ENST00000344113|Transcript|intron_variant&feature_truncation|||||SYNE2|protein_coding|||||||;GR=0.536;PH=0.538;PS=0.005;REPMASK=DNA GT:GL:GOF:GQ:NR:NV ./.:0,-0.14,-10.6:69:4:11:3 1/0:-9.56,0,-2.46:164:25:4:1 14 72743460 . C T 1920 PASS Source=Platypus;CSQ=T|ENSG00000182732|ENST00000555571|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000355512|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000406236|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000343854|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000553530|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000404301|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000553525|Transcript|intron_variant|||||RGS6|protein_coding|YES||||||,T|ENSG00000182732|ENST00000556437|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000402788|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000407322|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000554474|Transcript|intron_variant&NMD_transcript_variant|||||RGS6|nonsense_mediated_decay|||||||;GR=-0.451;PH=-1.955;PS=0.041;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-31.72,0,-221.32:5:99:82:15 0/0:0,-7.4,-300:1:74:97:6 14 72945327 . C T 483 PASS Source=Platypus;CSQ=T|ENSG00000182732|ENST00000555368|Transcript|downstream_gene_variant||||288|RGS6|processed_transcript|||||||,T|ENSG00000182732|ENST00000553690|Transcript|downstream_gene_variant||||4550|RGS6|processed_transcript|||||||,T|ENSG00000182732|ENST00000406236|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000553530|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000553525|Transcript|intron_variant|||||RGS6|protein_coding|YES||||||,T|ENSG00000182732|ENST00000556437|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000554782|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000407322|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000555571|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000355512|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000404301|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000434263|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000554734|Transcript|downstream_gene_variant||||1359|RGS6|retained_intron|||||||,T|ENSG00000182732|ENST00000343854|Transcript|intron_variant|||||RGS6|protein_coding|||||||,T|ENSG00000182732|ENST00000554474|Transcript|intron_variant&NMD_transcript_variant|||||RGS6|nonsense_mediated_decay|||||||,T|ENSG00000182732|ENST00000402788|Transcript|intron_variant|||||RGS6|protein_coding|||||||;GR=1.8;PH=0.541;PS=0.34 GT:GL:GOF:GQ:NR:NV 1/1:-220.1,-13.85,0:17:99:47:43 1/1:-196.6,-12.34,0:6:99:42:40 14 73907998 . C T 617 PASS Source=Platypus;CSQ=T|ENSG00000133961|ENST00000554818|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000356296|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000557031|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|processed_transcript|||||||,T|ENSG00000133961|ENST00000555394|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000553415|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|processed_transcript|||||||,T|ENSG00000133961|ENST00000554315|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|retained_intron|||||||,T|ENSG00000133961|ENST00000556112|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|retained_intron|||||||,T|ENSG00000133961|ENST00000557597|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000556700|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|processed_transcript|||||||,T|ENSG00000133961|ENST00000355058|Transcript|intron_variant|||||NUMB|protein_coding|YES||||||,T|ENSG00000133961|ENST00000535282|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000554546|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000359560|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000555238|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000555307|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000554394|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000556600|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|processed_transcript|||||||,T|ENSG00000133961|ENST00000555987|Transcript|intron_variant|||||NUMB|protein_coding|||||||,T|ENSG00000133961|ENST00000557774|Transcript|intron_variant&non_coding_transcript_variant|||||NUMB|retained_intron|||||||;GR=0.453;PH=0.497;PS=0.306;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-223.4,-18.57,0:2:99:65:65 1/0:-58.86,0,-75.46:1:99:44:19 14 75036731 . C T 1580 PASS Source=Platypus;CSQ=T|ENSG00000119681|ENST00000556359|Transcript|intron_variant|||||LTBP2|protein_coding|||||||,T|ENSG00000119681|ENST00000557425|Transcript|intron_variant&non_coding_transcript_variant|||||LTBP2|processed_transcript|||||||,T|ENSG00000119681|ENST00000261978|Transcript|intron_variant|||||LTBP2|protein_coding|YES||||||,T|ENSG00000119681|ENST00000556690|Transcript|intron_variant|||||LTBP2|protein_coding|||||||,T|ENSG00000119681|ENST00000553939|Transcript|intron_variant&NMD_transcript_variant|||||LTBP2|nonsense_mediated_decay|||||||;GR=0.862;PH=0.213;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-82.3,0,-59.9:4:99:53:27 1/1:-151.9,-12.64,0:2:99:44:43 14 75866647 . A G 1049 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.36;PH=0.662;PS=0.003 GT:GL:GOF:GQ:NR:NV ./.:-3.7,0,0:0:3:0:0 1/1:-11.8,-0.78,0:0:8:4:4 14 78718623 . T C 1918 PASS Source=Platypus;CSQ=C|ENSG00000021645|ENST00000556088|Transcript|intron_variant&non_coding_transcript_variant|||||NRXN3|retained_intron|||||||,C|ENSG00000021645|ENST00000554738|Transcript|intron_variant&NMD_transcript_variant|||||NRXN3|nonsense_mediated_decay|||||||;GR=0.832;PH=0.283;PS=0.002;UK10K=1/7562 GT:GL:GOF:GQ:NR:NV 1/0:-118.73,0,-93.63:22:99:74:40 0/0:0,-12.64,-159.5:10:99:45:0 14 79128290 . T C 817 PASS Source=Platypus;CSQ=C|ENSG00000021645|ENST00000554719|Transcript|intron_variant|||||NRXN3|protein_coding|YES||||||,C|ENSG00000021645|ENST00000556496|Transcript|intron_variant&non_coding_transcript_variant|||||NRXN3|retained_intron|||||||,C|ENSG00000021645|ENST00000553631|Transcript|intron_variant|||||NRXN3|protein_coding|||||||,C|ENSG00000021645|ENST00000554738|Transcript|intron_variant&NMD_transcript_variant|||||NRXN3|nonsense_mediated_decay|||||||,C|ENSG00000021645|ENST00000335750|Transcript|intron_variant|||||NRXN3|protein_coding|||||||;GR=0.149;PH=0.166;PS=0.018;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-4.22,-108.22:5:42:43:8 1/0:-6.63,0,-77.04:2:66:34:9 14 81427854 . G A 1210 PASS Source=Platypus;CSQ=A|ENSG00000165409|ENST00000342443|Transcript|intron_variant|||||TSHR|protein_coding|||||||,A|ENSG00000100629|ENST00000555529|Transcript|upstream_gene_variant||||2026|CEP128|protein_coding|||||||,A|ENSG00000100629|ENST00000556800|Transcript|upstream_gene_variant||||2004|CEP128|retained_intron|||||||,A|ENSG00000165409|ENST00000541158|Transcript|intron_variant|||||TSHR|protein_coding|YES||||||,A|ENSG00000165409|ENST00000553763|Transcript|intron_variant&non_coding_transcript_variant|||||TSHR|retained_intron|||||||,A|ENSG00000165409|ENST00000554263|Transcript|intron_variant|||||TSHR|protein_coding|||||||,A|ENSG00000100629|ENST00000554368|Transcript|upstream_gene_variant||||1993|CEP128|processed_transcript|||||||,A|ENSG00000165409|ENST00000554435|Transcript|intron_variant|||||TSHR|protein_coding|||||||,A|ENSG00000100629|ENST00000556042|Transcript|upstream_gene_variant||||2009|CEP128|protein_coding|||||||,A|ENSG00000100629|ENST00000556981|Transcript|upstream_gene_variant||||2006|CEP128|protein_coding|||||||,A|ENSG00000165409|ENST00000555326|Transcript|intron_variant&NMD_transcript_variant|||||TSHR|nonsense_mediated_decay|||||||,A|ENSG00000165409|ENST00000298171|Transcript|intron_variant|||||TSHR|protein_coding|||||||;GR=1.11;PH=0.416;PS=0.489;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-78.09,0,-101.99:4:99:65:29 0/1:-83.41,0,-83.51:8:99:60:32 14 82301458 . A G 197 PASS Source=Platypus;CSQ=G|ENSG00000259035|ENST00000554814|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-666E17.1|lincRNA|YES||||||;GR=0.235;PH=0.263;PS=0.119;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-226.8,-18.64,0:1:99:64:64 1/1:-206.7,-16.52,0:1:99:58:58 14 84434713 . C T 913 PASS Source=Platypus;CSQ=T||ENSR00000421809|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,T||||intergenic_variant|||||||||||||;GR=0.149;PH=0.192;PS=0.04;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-183.6,-14.84,0:4:99:53:53 1/1:-146.2,-11.44,0:0:99:40:40 14 85199126 . C T 1553 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-2.29;PH=-0.591;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-90.15,0,-68.85:11:99:55:30 1/0:-66.6,0,-113.5:11:99:60:24 14 87002443 . G A 1443 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-3.85;PH=-1.102;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-235.9,-19.27,0:1:99:66:66 0/1:-76.65,0,-75.75:2:99:52:26 14 88242179 . C T 1426 PASS Source=Platypus;CSQ=T|ENSG00000258807|ENST00000554305|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-1152H15.1|lincRNA|YES||||||,T|ENSG00000258807|ENST00000554519|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-1152H15.1|lincRNA|||||||;GR=0.0465;PH=0.132;PS=0.126;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-69.75,0,-89.95:1:99:55:25 1/1:-169.2,-13.85,0:1:99:47:47 14 92908010 . C T 1150 PASS Source=Platypus;CSQ=T|ENSG00000140090|ENST00000393265|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000532405|Transcript|intron_variant|||||SLC24A4|protein_coding|YES||||||,T|ENSG00000140090|ENST00000554461|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000531433|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000525557|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000298877|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000351924|Transcript|intron_variant|||||SLC24A4|protein_coding|||||||,T|ENSG00000140090|ENST00000554925|Transcript|upstream_gene_variant||||1699|SLC24A4|retained_intron|||||||;GR=2.92;PH=1.927;PS=0.008;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.64,-196.9:8:99:51:15 1/1:-179.9,-10.24,0:7:99:47:34 14 93094075 . G A 2555 PASS Source=Platypus;CSQ=A|ENSG00000100599|ENST00000554888|Transcript|intron_variant&non_coding_transcript_variant|||||RIN3|processed_transcript|||||||,A|ENSG00000100599|ENST00000418924|Transcript|intron_variant&non_coding_transcript_variant|||||RIN3|processed_transcript|||||||,A|ENSG00000100599|ENST00000216487|Transcript|intron_variant|||||RIN3|protein_coding|YES||||||,A|ENSG00000100599|ENST00000555589|Transcript|intron_variant&NMD_transcript_variant|||||RIN3|nonsense_mediated_decay|||||||;GR=0.158;PH=0.202;PS=0.022;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-165.5,-14.13,0:2:99:50:50 1/1:-213,-17.46,0:1:99:60:60 14 96482580 . TTCC - 237 PASS Source=Platypus;CSQ=-|ENSG00000271358|ENST00000603288|Transcript|upstream_gene_variant||||3238|RP11-241N4.2|processed_pseudogene|YES||||||;GR=-1.17;PH=-0.302;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-133.65,0,-66.15:6:99:65:41 1/0:-100.27,0,-102.97:5:99:66:33 14 97985529 . AT - 170 PASS Source=Platypus;CSQ=-|ENSG00000246084|ENST00000554862|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTD-2506J14.1|lincRNA|||||||;GR=1.68;PH=0.368;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.65,-298.19:1:99:49:0 0/1:-63.48,0,-298.49:18:99:60:5 14 103199463 . G A 223 PASS Source=Platypus;CSQ=A|ENSG00000089902|ENST00000262241|Transcript|downstream_gene_variant||||2550|RCOR1|protein_coding|YES||||||,A|ENSG00000089902|ENST00000570597|Transcript|downstream_gene_variant||||2551|RCOR1|protein_coding|||||||;GR=0.288;PH=0.097;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-54.2,-4.49,0:3:45:17:17 1/0:-19.18,0,-52.18:1:99:24:7 14 105717866 . T C 2764 PASS Source=Platypus;CSQ=C|ENSG00000185024|ENST00000550208|Transcript|upstream_gene_variant||||2618|BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000379937|Transcript|intron_variant|||||BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000550375|Transcript|upstream_gene_variant||||2990|BRF1|protein_coding|||||||,C|ENSG00000184887|ENST00000392553|Transcript|downstream_gene_variant||||1233|BTBD6|retained_intron|||||||,C|ENSG00000185024|ENST00000550692|Transcript|downstream_gene_variant||||986|BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000552127|Transcript|upstream_gene_variant||||2137|BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000546417|Transcript|intron_variant|||||BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000392557|Transcript|upstream_gene_variant||||3635|BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000446501|Transcript|upstream_gene_variant||||2125|BRF1|protein_coding|||||||,C|ENSG00000184887|ENST00000536364|Transcript|downstream_gene_variant||||445|BTBD6|protein_coding|||||||,C|ENSG00000185024|ENST00000551787|Transcript|upstream_gene_variant||||4336|BRF1|protein_coding|||||||,C|ENSG00000185024|ENST00000379932|Transcript|upstream_gene_variant||||4336|BRF1|protein_coding|||||||,C|ENSG00000184887|ENST00000392554|Transcript|downstream_gene_variant||||436|BTBD6|protein_coding|YES||||||,C|ENSG00000185024|ENST00000546474|Transcript|intron_variant|||||BRF1|protein_coding|YES||||||,C|ENSG00000184887|ENST00000537513|Transcript|downstream_gene_variant||||1092|BTBD6|protein_coding|||||||,C|ENSG00000185024|ENST00000548421|Transcript|downstream_gene_variant||||4659|BRF1|protein_coding|||||||,C|ENSG00000184887|ENST00000327471|Transcript|downstream_gene_variant||||445|BTBD6|protein_coding|||||||,C|ENSG00000185024|ENST00000327359|Transcript|intron_variant|||||BRF1|protein_coding|||||||,C|ENSG00000184887|ENST00000463376|Transcript|downstream_gene_variant||||436|BTBD6|protein_coding|||||||,C|ENSG00000185024|ENST00000440513|Transcript|intron_variant|||||BRF1|protein_coding|||||||;GR=1.76;PH=1.078;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.52,-164.7:2:99:46:1 1/1:-183,-15,0:0:99:53:52 15 22965134 . G A 1159 PASS Source=Platypus;CSQ=A|ENSG00000068793|ENST00000558826|Transcript|intron_variant&non_coding_transcript_variant|||||CYFIP1|retained_intron|||||||,A|ENSG00000068793|ENST00000435939|Transcript|intron_variant|||||CYFIP1|protein_coding|||||||,A|ENSG00000068793|ENST00000561020|Transcript|upstream_gene_variant||||2494|CYFIP1|retained_intron|||||||,A|ENSG00000068793|ENST00000561296|Transcript|downstream_gene_variant||||1260|CYFIP1|retained_intron|||||||,A|ENSG00000068793|ENST00000560848|Transcript|intron_variant|||||CYFIP1|protein_coding|||||||,A|ENSG00000068793|ENST00000313077|Transcript|intron_variant|||||CYFIP1|protein_coding|YES||||||;GR=-0.509;PH=-0.282;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-107.04,0,-75.54:16:99:65:38 1/1:-214.3,-17.46,0:24:99:59:59 15 23846427 . CTCT - 918 PASS Source=Platypus;CSQ=-|ENSG00000179455|ENST00000568945|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MKRN3|processed_transcript|||||||,-|ENSG00000179455|ENST00000568252|Transcript|intron_variant&feature_truncation|||||MKRN3|protein_coding|||||||;GR=0.122;PH=0.193;PS=0.007;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-217.9:2:99:64:0 0/1:-61.75,0,-84.55:1:99:48:21 15 23880233 . G A 629 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.225;PH=0.3;PS=0.018;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-29.72,0,-16.92:3:99:48:15 1/1:-82.3,-10.34,0:2:99:49:33 15 24803616 . AG - 286 PASS Source=Platypus;CSQ=-|ENSG00000259905|ENST00000569908|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|312-313||||PWRN1|lincRNA|||||||,-|ENSG00000259905|ENST00000568045|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||,-|ENSG00000259905|ENST00000567647|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||,-|ENSG00000259905|ENST00000565295|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||,-|ENSG00000259905|ENST00000568609|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|YES||||||,-|ENSG00000259905|ENST00000565241|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||;GR=-0.317;PH=-1.232;PS=0.003;REPMASK=LTR;SD=0.967087 GT:GL:GOF:GQ:NR:NV 0/1:-86.17,0,-93.17:14:99:62:29 1/1:-233.7,-18.66,0:0:99:63:63 15 24872627 . TTTC - 1912 PASS Source=Platypus;CSQ=-|ENSG00000259905|ENST00000568019|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||,-|ENSG00000259905|ENST00000564898|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PWRN1|lincRNA|||||||;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-58.71,-181.5:2:99:54:0 1/1:-183.1,-14.45,0:3:99:50:50 15 25477999 . A G 2077 PASS Source=Platypus;CSQ=G|ENSG00000200593|ENST00000363723|Transcript|downstream_gene_variant||||1933|SNORD115-33|snoRNA|YES||||||,G|ENSG00000202499|ENST00000365629|Transcript|upstream_gene_variant||||3233|SNORD115-36|snoRNA|YES||||||,G|ENSG00000200949|ENST00000364079|Transcript|downstream_gene_variant||||3804|SNORD115-32|snoRNA|YES||||||,G|ENSG00000224078|ENST00000453082|Transcript|intron_variant&non_coding_transcript_variant|||||SNHG14|antisense|||||||,G|ENSG00000201992|ENST00000365122|Transcript|upstream_gene_variant||||1395|SNORD115-35|snoRNA|YES||||||,G|ENSG00000199311|ENST00000362441|Transcript|downstream_gene_variant||||384|SNORD115-34|snoRNA|YES||||||;GR=0.122;PH=0.166;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.56,-204.3:2:99:57:0 1/1:-144.7,-11.44,0:22:99:42:42 15 25651850 . CAC - 2721 PASS Source=Platypus;CSQ=-|ENSG00000224078|ENST00000554726|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SNHG14|antisense|||||||,-|ENSG00000114062|ENST00000566215|Transcript|intron_variant&feature_truncation|||||UBE3A|protein_coding|||||||,-|ENSG00000114062|ENST00000397954|Transcript|intron_variant&feature_truncation|||||UBE3A|protein_coding|YES||||||,-|ENSG00000114062|ENST00000438097|Transcript|upstream_gene_variant||||1197|UBE3A|protein_coding|||||||,-|ENSG00000114062|ENST00000428984|Transcript|intron_variant&feature_truncation|||||UBE3A|protein_coding|||||||,-|ENSG00000114062|ENST00000232165|Transcript|intron_variant&feature_truncation|||||UBE3A|protein_coding|||||||;GR=-0.649;PH=-0.503;PS=0.003;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/0:0,-7.53,-110.2:9:75:29:0 1/0:-61.17,0,-45.87:20:99:33:17 15 25838364 . GGT - 602 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.263;PH=0.39;PS=0.113;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-14.15,-172.2:6:99:51:0 1/0:-51.25,0,-108.55:4:99:52:18 15 26719895 . C T 1095 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.213;PH=-0.065;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-57.59,0,-91.59:1:99:52:21 0/0:0,-14.15,-168.3:1:99:48:0 15 27729215 . G A 2736 PASS Source=Platypus;CSQ=A|ENSG00000182256|ENST00000554696|Transcript|intron_variant|||||GABRG3|protein_coding|||||||,A|ENSG00000182256|ENST00000555083|Transcript|downstream_gene_variant||||2732|GABRG3|protein_coding|||||||,A|ENSG00000182256|ENST00000333743|Transcript|intron_variant|||||GABRG3|protein_coding|YES||||||,A|ENSG00000259168|ENST00000556642|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-100M12.3|antisense|||||||;GR=0.235;PH=0.308;PS=0.099;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.55,-92:1:99:53:0 1/0:-45.64,0,-47.14:2:99:68:21 15 29945194 . AGA - 2038 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.985;PH=0.689;PS=0.003;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-225.6,-18.66,0:2:99:62:62 1/1:-136.3,-11.1,0:4:99:38:38 15 31409047 . G A 2317 PASS Source=Platypus;CSQ=A|ENSG00000134160|ENST00000558445|Transcript|intron_variant|||||TRPM1|protein_coding|||||||,A|ENSG00000134160|ENST00000542188|Transcript|intron_variant|||||TRPM1|protein_coding|YES||||||,A|ENSG00000134160|ENST00000559177|Transcript|intron_variant|||||TRPM1|protein_coding|||||||;GR=0.158;PH=0.202;PS=0.144;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-73.04,0,-98.44:27:99:59:26 0/0:0,-13.85,-174.1:1:99:48:1 15 33099384 . GA - 516 PASS Source=Platypus;CSQ=-|ENSG00000248905|ENST00000559047|Transcript|intron_variant&feature_truncation|||||FMN1|protein_coding|||||||,-|ENSG00000248905|ENST00000558882|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FMN1|processed_transcript|||||||,-|ENSG00000248905|ENST00000561249|Transcript|intron_variant&feature_truncation|||||FMN1|protein_coding|||||||,-|ENSG00000248905|ENST00000334528|Transcript|intron_variant&feature_truncation|||||FMN1|protein_coding|YES||||||,-|ENSG00000248905|ENST00000559610|Transcript|downstream_gene_variant||||3711|FMN1|protein_coding|||||||;GR=-1.1;PH=-0.183;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-82.8,0,-70:2:99:56:28 1/0:-61.57,0,-88.07:1:99:53:24 15 34093452 . AG - 1193 PASS Source=Platypus;CSQ=-|ENSG00000198838|ENST00000389232|Transcript|intron_variant&feature_truncation|||||RYR3|protein_coding|YES||||||,-|ENSG00000198838|ENST00000415757|Transcript|intron_variant&feature_truncation|||||RYR3|protein_coding|||||||;GR=0.235;PH=0.263;PS=0.052;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-112.7,-9.03,0:1:90:30:30 0/1:-53.06,0,-78.76:2:99:43:18 15 34711856 . C T 1312 PASS Source=Platypus;CSQ=T|ENSG00000175265|ENST00000565885|Transcript|intron_variant&non_coding_transcript_variant|||||GOLGA8A|processed_transcript|||||||,T|ENSG00000175265|ENST00000569781|Transcript|intron_variant&non_coding_transcript_variant|||||GOLGA8A|processed_transcript|||||||,T|ENSG00000175265|ENST00000543376|Transcript|intron_variant|||||GOLGA8A|protein_coding|||||||;GR=0.203;PH=0.074;PS=0.001;SD=0.9893 GT:GL:GOF:GQ:NR:NV 1/0:-0.32,0,-2.42:2:5:13:1 1/1:-3.1,-0.11,0:1:4:15:6 15 35521394 . T C 2377 PASS Source=Platypus;CSQ=C|ENSG00000134146|ENST00000560386|Transcript|intron_variant&non_coding_transcript_variant|||||DPH6|processed_transcript|||||||,C|ENSG00000259516|ENST00000560832|Transcript|intron_variant&non_coding_transcript_variant|||||ANP32AP1|processed_transcript|YES||||||;PH=0.103;PS=0.312;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-124.92,0,-109.62:6:99:51:18 0/0:0,-13.22,-232.5:2:99:54:1 15 38413113 . G A 1324 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.371;PH=-0.722;PS=0.584;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-136,-11.66,0:2:99:42:42 1/1:-123.9,-10.49,0:5:99:37:37 15 39455889 . T C 939 PASS Source=Platypus;CSQ=C|ENSG00000259345|ENST00000561058|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-624L4.1|antisense|||||||,C|ENSG00000259423|ENST00000560259|Transcript|upstream_gene_variant||||4120|RP11-265N7.2|lincRNA|||||||,C|ENSG00000259345|ENST00000558209|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-624L4.1|antisense|||||||,C|ENSG00000259423|ENST00000558255|Transcript|upstream_gene_variant||||4051|RP11-265N7.2|lincRNA|YES||||||,C|ENSG00000259345|ENST00000560484|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-624L4.1|antisense|||||||;GR=0.401;PH=0.369;PS=0.022;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-194,-16.54,0:3:99:62:62 1/0:-89.55,0,-59.55:1:99:52:30 15 49187106 . C T 2726 PASS Source=Platypus;CSQ=T|ENSG00000185634|ENST00000332408|Transcript|intron_variant|||||SHC4|protein_coding|YES||||||;GR=-0.456;PH=-0.21;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-9.33,-116.1:3:93:35:0 1/0:-53.07,0,-40.87:12:99:31:17 15 50171930 . C T 662 PASS Source=Platypus;CSQ=T|ENSG00000104043|ENST00000557955|Transcript|intron_variant&NMD_transcript_variant|||||ATP8B4|nonsense_mediated_decay|||||||,T|ENSG00000104043|ENST00000559829|Transcript|intron_variant|||||ATP8B4|protein_coding|||||||,T|ENSG00000104043|ENST00000558906|Transcript|intron_variant&NMD_transcript_variant|||||ATP8B4|nonsense_mediated_decay|||||||,T|ENSG00000259188|ENST00000558150|Transcript|upstream_gene_variant||||692|CTD-2647E9.3|antisense|||||||,T|ENSG00000259188|ENST00000560375|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|130||||CTD-2647E9.3|antisense|YES||||||,T|ENSG00000104043|ENST00000560161|Transcript|downstream_gene_variant||||3426|ATP8B4|processed_transcript|||||||,T|ENSG00000104043|ENST00000560479|Transcript|intron_variant|||||ATP8B4|protein_coding|||||||,T|ENSG00000104043|ENST00000559726|Transcript|intron_variant&NMD_transcript_variant|||||ATP8B4|nonsense_mediated_decay|||||||,T|ENSG00000104043|ENST00000284509|Transcript|intron_variant|||||ATP8B4|protein_coding|YES||||||,T|ENSG00000104043|ENST00000558203|Transcript|upstream_gene_variant||||145|ATP8B4|retained_intron|||||||,T|ENSG00000104043|ENST00000560354|Transcript|upstream_gene_variant||||3127|ATP8B4|retained_intron|||||||,T|ENSG00000104043|ENST00000558498|Transcript|upstream_gene_variant||||3038|ATP8B4|protein_coding|||||||;GR=-0.525;PH=-0.075;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-106.4,-9.31,0:6:93:32:32 1/1:-142,-11.74,0:3:99:40:40 15 53649001 . C T 2896 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.19;PH=1.009;PS=0.006;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-111.9,-9.56,0:91:96:32:32 1/1:-127.4,-10.54,0:50:99:36:36 15 54607440 . CC - 677 PASS Source=Platypus;CSQ=-|ENSG00000137766|ENST00000561210|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||UNC13C|retained_intron|||||||,-|ENSG00000137766|ENST00000537900|Transcript|intron_variant&feature_truncation|||||UNC13C|protein_coding|||||||,-|ENSG00000137766|ENST00000545554|Transcript|intron_variant&feature_truncation|||||UNC13C|protein_coding|||||||,-|ENSG00000137766|ENST00000260323|Transcript|intron_variant&feature_truncation|||||UNC13C|protein_coding|YES||||||;GR=-4.66;PH=-1.267;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.02,-162.4:7:99:49:1 1/1:-185.4,-16.17,0:17:99:57:57 15 55213115 . AGTT - 1557 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.149;PS=0.027;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-8.98,0,-161.78:67:90:58:7 0/0:0,-8.5,-176.1:38:85:52:2 15 59025765 . A G 1807 PASS Source=Platypus;CSQ=G|ENSG00000137845|ENST00000559053|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000560608|Transcript|intron_variant&non_coding_transcript_variant|||||ADAM10|processed_transcript|||||||,G|ENSG00000137845|ENST00000396140|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000561149|Transcript|intron_variant&non_coding_transcript_variant|||||ADAM10|processed_transcript|||||||,G|ENSG00000137845|ENST00000558004|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000402627|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000439637|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000260408|Transcript|intron_variant|||||ADAM10|protein_coding|YES||||||,G|ENSG00000137845|ENST00000561288|Transcript|intron_variant|||||ADAM10|protein_coding|||||||,G|ENSG00000137845|ENST00000558733|Transcript|intron_variant&non_coding_transcript_variant|||||ADAM10|processed_transcript|||||||,G|ENSG00000137845|ENST00000497846|Transcript|intron_variant&non_coding_transcript_variant|||||ADAM10|processed_transcript|||||||;GR=-0.397;PH=-0.764;PS=0.063;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-163.8,-13.83,0:22:99:50:50 1/1:-161.3,-14.07,0:20:99:51:51 15 62262622 . A G 1092 PASS Source=Platypus;CSQ=G|ENSG00000129003|ENST00000261517|Transcript|intron_variant|||||VPS13C|protein_coding|YES||||||,G|ENSG00000129003|ENST00000395896|Transcript|intron_variant|||||VPS13C|protein_coding|||||||,G|ENSG00000129003|ENST00000249837|Transcript|intron_variant|||||VPS13C|protein_coding|||||||,G|ENSG00000129003|ENST00000395898|Transcript|intron_variant|||||VPS13C|protein_coding|||||||;GR=1.43;PH=0.912;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-85.47,0,-87.62:39:99:53:26 0/0:0,-12.93,-167:3:99:46:0 15 63212331 . A G 2786 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.01;PH=0.705;PS=0.037 GT:GL:GOF:GQ:NR:NV 1/0:-1,-1,-1:52:99:20,20:8,8 2/0:-1,-1,-1:71:99:40,38:15,14 15 64382763 . C T 1190 PASS Source=Platypus;CSQ=T|ENSG00000166797|ENST00000559705|Transcript|intron_variant&NMD_transcript_variant|||||FAM96A|nonsense_mediated_decay|||||||,T|ENSG00000028528|ENST00000559061|Transcript|upstream_gene_variant||||3712|SNX1|protein_coding|||||||,T|ENSG00000166797|ENST00000559950|Transcript|intron_variant|||||FAM96A|protein_coding|||||||,T|ENSG00000166797|ENST00000300030|Transcript|intron_variant|||||FAM96A|protein_coding|YES||||||,T|ENSG00000166797|ENST00000380290|Transcript|intron_variant|||||FAM96A|protein_coding|||||||,T|ENSG00000028528|ENST00000560829|Transcript|upstream_gene_variant||||3559|SNX1|protein_coding|||||||,T|ENSG00000166797|ENST00000557835|Transcript|intron_variant|||||FAM96A|protein_coding|||||||,T||ENSR00000409582|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-4.72;PH=-1.624;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-160,-13.25,0:4:99:45:45 1/1:-215.1,-17.46,0:1:99:59:59 15 64912811 . T C 852 PASS Source=Platypus;CSQ=C|ENSG00000180357|ENST00000326648|Transcript|intron_variant|||||ZNF609|protein_coding|YES||||||,C|ENSG00000180357|ENST00000558680|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF609|processed_transcript|||||||,C||ENSR00000409645|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=4.08;PH=0.824;PS=0.998 GT:GL:GOF:GQ:NR:NV 1/1:-196.7,-16.53,0:2:99:58:58 0/0:0,-13.85,-168.8:2:99:48:0 15 71780027 . TTG - 1928 PASS Source=Platypus;CSQ=-|ENSG00000187720|ENST00000355327|Transcript|intron_variant&feature_truncation|||||THSD4|protein_coding|YES||||||,-|ENSG00000187720|ENST00000261862|Transcript|intron_variant&feature_truncation|||||THSD4|protein_coding|||||||;GR=0.917;PH=0.241;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.96,-287.1:1:99:65:0 1/0:-105.44,0,-114.34:4:99:61:25 15 73701469 . T C 2116 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.838;PH=0.159;PS=0.005 GT:GL:GOF:GQ:NR:NV 1/1:-153.03,-5.29,0:26:53:25:22 1/1:-176.8,-5.94,0:32:59:30:23 15 77205053 . C T 987 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.403;PH=0.463;PS=0.261;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-1.3,-0.15,0:63:4:10:9 1/0:-4.84,0,-3.84:38:38:9:5 15 79563509 . A G 2933 PASS Source=Platypus;CSQ=G|ENSG00000259234|ENST00000560872|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000560533|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|YES||||||,G|ENSG00000259234|ENST00000559225|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000559979|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000560452|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000557790|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000558297|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||,G|ENSG00000259234|ENST00000560732|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-17L5.4|lincRNA|||||||;GR=1.54;PH=0.962;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.36,-223.7:7:99:64:0 1/0:-77.54,0,-97.84:0:99:57:25 15 81373700 . CC - 2479 PASS Source=Platypus;CSQ=-|ENSG00000156206|ENST00000560091|Transcript|intron_variant&feature_truncation|||||C15orf26|protein_coding|||||||;GR=1.2;PH=0.454;PS=0.002;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-157.03,0,-258.03:6:99:69:26 1/0:-197.24,0,-201.24:1:99:65:31 15 83955856 . TGTG - 123 PASS Source=Platypus;CSQ=-|ENSG00000259986|ENST00000565495|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-382A20.4|antisense|||||||,-|ENSG00000169594|ENST00000345382|Transcript|upstream_gene_variant||||2390|BNC1|protein_coding|YES||||||,-|ENSG00000169594|ENST00000569704|Transcript|upstream_gene_variant||||3785|BNC1|protein_coding|||||||,-||ENSR00000412544|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-2.12;PH=-0.464;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-64,0,-84.9:2:99:52:23 0/0:0,-9.76,-111.5:4:98:36:0 15 85141443 . GT - 561 PASS Source=Platypus;CSQ=-|ENSG00000176371|ENST00000546148|Transcript|upstream_gene_variant||||2802|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000448803|Transcript|upstream_gene_variant||||2792|ZSCAN2|protein_coding|YES||||||,-|ENSG00000176371|ENST00000358472|Transcript|upstream_gene_variant||||2807|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000502939|Transcript|upstream_gene_variant||||2810|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000540936|Transcript|upstream_gene_variant||||2773|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000334141|Transcript|upstream_gene_variant||||2805|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000442073|Transcript|upstream_gene_variant||||2803|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000379358|Transcript|upstream_gene_variant||||2837|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000327179|Transcript|upstream_gene_variant||||2837|ZSCAN2|protein_coding|||||||,-|ENSG00000176371|ENST00000546275|Transcript|upstream_gene_variant||||2796|ZSCAN2|protein_coding|||||||,-||ENSR00000022664|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-3.36;PH=-0.731;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-25.07,0,-1.73:5:17:48:7 1/1:-40.95,-7.91,0:2:79:30:12 15 85962599 . T C 2265 PASS Source=Platypus;CSQ=C|ENSG00000170776|ENST00000560302|Transcript|intron_variant|||||AKAP13|protein_coding|||||||,C|ENSG00000170776|ENST00000394518|Transcript|intron_variant|||||AKAP13|protein_coding|||||||,C|ENSG00000170776|ENST00000559362|Transcript|intron_variant|||||AKAP13|protein_coding|||||||,C|ENSG00000170776|ENST00000560256|Transcript|intron_variant|||||AKAP13|protein_coding|||||||,C|ENSG00000170776|ENST00000361243|Transcript|intron_variant|||||AKAP13|protein_coding|YES||||||,C|ENSG00000259630|ENST00000559487|Transcript|downstream_gene_variant||||3735|CTD-2262B20.1|transcribed_processed_pseudogene|YES||||||,C||ENSR00001454678|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.54;PH=0.551;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-220.4,-18.06,0:4:99:63:63 0/1:-96.89,0,-96.49:1:99:63:32 15 88700973 . T C 1936 PASS Source=Platypus;CSQ=C|ENSG00000140538|ENST00000317501|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000559188|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000558676|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000557856|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000540489|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000394480|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000542733|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000357724|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000355254|Transcript|intron_variant|||||NTRK3|protein_coding|||||||,C|ENSG00000140538|ENST00000360948|Transcript|intron_variant|||||NTRK3|protein_coding|YES||||||;GR=-1.78;PH=-0.456;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-50.06,0,-70.36:3:99:43:19 0/1:-67.45,0,-86.05:4:99:56:25 15 89045466 . T C 630 PASS Source=Platypus;CSQ=C|ENSG00000271997|ENST00000606927|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3553||||RP11-97O12.6|sense_intronic|YES||||||,C|ENSG00000173867|ENST00000606219|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-97O12.7|processed_transcript|YES||||||,C|ENSG00000173867|ENST00000561140|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-97O12.7|processed_transcript|||||||;GR=-2.27;PH=-0.711;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-213.5,-18.25,0:3:99:62:62 1/1:-166.9,-13.8,0:4:99:48:48 15 89186694 rs554424885 G A 755 PASS Source=Platypus;CSQ=A|ENSG00000172183|ENST00000557824|Transcript|upstream_gene_variant||||3449|ISG20|retained_intron|||||||,A|ENSG00000172183|ENST00000560573|Transcript|intron_variant&non_coding_transcript_variant|||||ISG20|retained_intron|||||||,A|ENSG00000172183|ENST00000558942|Transcript|intron_variant&non_coding_transcript_variant|||||ISG20|retained_intron|||||||,A|ENSG00000172183|ENST00000379224|Transcript|intron_variant|||||ISG20|protein_coding|||||||,A|ENSG00000172183|ENST00000559876|Transcript|intron_variant|||||ISG20|protein_coding|||||||,A|ENSG00000172183|ENST00000560741|Transcript|intron_variant|||||ISG20|protein_coding|||||||,A|ENSG00000172183|ENST00000306072|Transcript|intron_variant|||||ISG20|protein_coding|YES||||||,A|ENSG00000172183|ENST00000558236|Transcript|upstream_gene_variant||||4357|ISG20|processed_transcript|||||||;GR=-0.47;PH=-0.818;PS=0.057;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/1:-177.8,-14.68,0:3:99:52:52 1/0:-69.84,0,-104.24:2:99:58:23 15 89665055 . AA - 1203 PASS Source=Platypus;CSQ=-|ENSG00000140526|ENST00000562073|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ABHD2|processed_transcript|||||||,-|ENSG00000140526|ENST00000352732|Transcript|intron_variant&feature_truncation|||||ABHD2|protein_coding|YES||||||,-|ENSG00000140526|ENST00000565066|Transcript|intron_variant&feature_truncation|||||ABHD2|protein_coding|||||||,-|ENSG00000140526|ENST00000565973|Transcript|intron_variant&feature_truncation|||||ABHD2|protein_coding|||||||,-|ENSG00000239151|ENST00000458793|Transcript|downstream_gene_variant||||984|RNU7-195P|snRNA|YES||||||,-|ENSG00000140526|ENST00000569411|Transcript|intron_variant&feature_truncation|||||ABHD2|protein_coding|||||||,-|ENSG00000140526|ENST00000355100|Transcript|intron_variant&feature_truncation|||||ABHD2|protein_coding|||||||,-||ENSR00001454995|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.613;PH=0.166;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-196.2,-13.15,0:6:99:45:37 1/1:-219.3,-14.65,0:4:99:55:45 15 93558669 . A G 1522 PASS Source=Platypus;CSQ=G|ENSG00000173575|ENST00000557381|Transcript|intron_variant|||||CHD2|protein_coding|||||||,G|ENSG00000173575|ENST00000394196|Transcript|intron_variant|||||CHD2|protein_coding|YES||||||,G|ENSG00000173575|ENST00000557759|Transcript|intron_variant|||||CHD2|protein_coding|||||||;GR=0.549;PH=0.144;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-10.81,-140.2:1:99:42:1 1/0:-72.67,0,-98.77:3:99:60:27 15 93965879 . T C 82 PASS Source=Platypus;CSQ=C|ENSG00000257060|ENST00000554105|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-266O8.1|lincRNA|||||||,C|ENSG00000257060|ENST00000543286|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-266O8.1|lincRNA|YES||||||,C|ENSG00000258909|ENST00000556708|Transcript|upstream_gene_variant||||74|RP11-164C12.2|lincRNA|YES||||||,C|ENSG00000257060|ENST00000553478|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-266O8.1|lincRNA|||||||,C|ENSG00000257060|ENST00000554466|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-266O8.1|lincRNA|||||||,C|ENSG00000257060|ENST00000556519|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-266O8.1|lincRNA|||||||;GR=1.37;PH=0.265;PS=0.957 GT:GL:GOF:GQ:NR:NV 0/1:-42.46,0,-121.46:29:99:60:18 0/1:-112.97,0,-106.57:38:99:73:37 15 96964152 . C T 1864 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.308;PH=0.04;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-87.07,0,-102.87:3:99:69:35 1/0:-64.15,0,-73.95:2:99:46:22 15 97494112 . T C 780 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.67;PH=0.085;PS=0.07 GT:GL:GOF:GQ:NR:NV 0/1:-83.3,0,-70.5:2:99:54:28 1/1:-204.9,-16.26,0:1:99:55:55 16 966098 . G A 1497 PASS Source=Platypus;CSQ=A|ENSG00000103227|ENST00000543238|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000260439|ENST00000567820|Transcript|upstream_gene_variant||||4935|LA16c-366D3.1|antisense|||||||,A|ENSG00000103227|ENST00000539379|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000562226|Transcript|intron_variant&NMD_transcript_variant|||||LMF1|nonsense_mediated_decay|||||||,A|ENSG00000103227|ENST00000399843|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000570014|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000566627|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000545827|Transcript|intron_variant&NMD_transcript_variant|||||LMF1|nonsense_mediated_decay|||||||,A|ENSG00000260439|ENST00000569574|Transcript|upstream_gene_variant||||4975|LA16c-366D3.1|antisense|YES||||||,A|ENSG00000103227|ENST00000568964|Transcript|intron_variant&NMD_transcript_variant|||||LMF1|nonsense_mediated_decay|||||||,A|ENSG00000103227|ENST00000568897|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000562380|Transcript|intron_variant|||||LMF1|protein_coding|||||||,A|ENSG00000103227|ENST00000567595|Transcript|intron_variant&NMD_transcript_variant|||||LMF1|nonsense_mediated_decay|||||||,A|ENSG00000103227|ENST00000262301|Transcript|intron_variant|||||LMF1|protein_coding|YES||||||;GR=-2.43;PH=-0.629;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-10.54,-179.3:2:99:36:0 0/1:-49.17,0,-74.27:4:99:29:12 16 1375896 . C T 2234 PASS Source=Platypus;CSQ=T|ENSG00000103275|ENST00000325437|Transcript|3_prime_UTR_variant|1709||||UBE2I|protein_coding|||||||,T|ENSG00000219274|ENST00000402520|Transcript|upstream_gene_variant||||3183|RPS20P2|processed_pseudogene|YES||||||,T|ENSG00000103275|ENST00000402301|Transcript|downstream_gene_variant||||4119|UBE2I|protein_coding|||||||,T|ENSG00000103275|ENST00000568989|Transcript|downstream_gene_variant||||1151|UBE2I|retained_intron|||||||,T|ENSG00000103275|ENST00000397515|Transcript|3_prime_UTR_variant|1986||||UBE2I|protein_coding|||||||,T|ENSG00000103275|ENST00000355803|Transcript|3_prime_UTR_variant|2130||||UBE2I|protein_coding|YES||||||,T|ENSG00000103275|ENST00000403747|Transcript|downstream_gene_variant||||681|UBE2I|protein_coding|||||||,T|ENSG00000261505|ENST00000567829|Transcript|upstream_gene_variant||||3050|LA16c-358B7.3|antisense|||||||,T|ENSG00000103275|ENST00000568288|Transcript|downstream_gene_variant||||1142|UBE2I|processed_transcript|||||||,T|ENSG00000103275|ENST00000397514|Transcript|3_prime_UTR_variant|1854||||UBE2I|protein_coding|||||||,T|ENSG00000103275|ENST00000406620|Transcript|downstream_gene_variant||||545|UBE2I|protein_coding|||||||,T|ENSG00000261505|ENST00000568106|Transcript|upstream_gene_variant||||3068|LA16c-358B7.3|antisense|YES||||||,T|ENSG00000103275|ENST00000566587|Transcript|downstream_gene_variant||||943|UBE2I|protein_coding|||||||,T||ENSR00000502245|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-2.34;PH=-3.483;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-215.2,-17.69,0:3:99:60:60 0/1:-97.84,0,-77.54:1:99:59:33 16 3105824 . T C 2039 PASS Source=Platypus;CSQ=C|ENSG00000008516|ENST00000570755|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant|||||MMP25|processed_transcript|||||||,C|ENSG00000261971|ENST00000576250|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|491||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573953|Transcript|downstream_gene_variant||||1316|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572574|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|661||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000597579|Transcript|upstream_gene_variant||||1048|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573130|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|410||||RP11-473M20.7|antisense|YES||||||,C|ENSG00000008516|ENST00000336577|Transcript|intron_variant|||||MMP25|protein_coding|YES||||||,C|ENSG00000261971|ENST00000572222|Transcript|downstream_gene_variant||||2038|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572930|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|197||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573878|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|271||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572427|Transcript|downstream_gene_variant||||2633|RP11-473M20.7|antisense|||||||,C|ENSG00000008516|ENST00000575441|Transcript|upstream_gene_variant||||971|MMP25|retained_intron|||||||,C|ENSG00000261971|ENST00000570949|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|287||||RP11-473M20.7|antisense|||||||;GR=0.0614;PH=-0.006;PS=0;SD=0.933677 GT:GL:GOF:GQ:NR:NV 1/0:-39.72,0,-37.02:2:99:72:35 1/1:-91.5,-14.5,0:6:99:64:50 16 3109170 . T C 2159 PASS Source=Platypus;CSQ=C|ENSG00000008516|ENST00000570755|Transcript|downstream_gene_variant||||3007|MMP25|processed_transcript|||||||,C|ENSG00000261971|ENST00000576250|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|195||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573953|Transcript|upstream_gene_variant||||722|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572574|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|202||||RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000597579|Transcript|upstream_gene_variant||||4394|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573130|Transcript|upstream_gene_variant||||2937|RP11-473M20.7|antisense|YES||||||,C|ENSG00000008516|ENST00000336577|Transcript|3_prime_UTR_variant|1997||||MMP25|protein_coding|YES||||||,C|ENSG00000261971|ENST00000572222|Transcript|upstream_gene_variant||||84|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572930|Transcript|upstream_gene_variant||||3150|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000573878|Transcript|upstream_gene_variant||||1972|RP11-473M20.7|antisense|||||||,C|ENSG00000261971|ENST00000572427|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|140||||RP11-473M20.7|antisense|||||||,C|ENSG00000008516|ENST00000575441|Transcript|downstream_gene_variant||||863|MMP25|retained_intron|||||||,C|ENSG00000261971|ENST00000570949|Transcript|upstream_gene_variant||||1956|RP11-473M20.7|antisense|||||||,C||ENSR00000050626|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.48;PH=0.412;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-66.94,0,-103.34:2:99:60:27 0/0:0,-13.25,-165.7:0:99:46:0 16 4473467 . CG - 1942 PASS Source=Platypus;CSQ=-|ENSG00000103423|ENST00000575106|Transcript|upstream_gene_variant||||2398|DNAJA3|nonsense_mediated_decay|||||||,-|ENSG00000103423|ENST00000262375|Transcript|upstream_gene_variant||||2338|DNAJA3|protein_coding|YES||||||,-|ENSG00000103423|ENST00000572974|Transcript|upstream_gene_variant||||2401|DNAJA3|processed_transcript|||||||,-|ENSG00000103423|ENST00000570857|Transcript|upstream_gene_variant||||2398|DNAJA3|nonsense_mediated_decay|||||||,-|ENSG00000103423|ENST00000576911|Transcript|upstream_gene_variant||||2398|DNAJA3|nonsense_mediated_decay|||||||,-|ENSG00000262246|ENST00000573165|Transcript|intron_variant&feature_truncation|||||CORO7|protein_coding|||||||,-|ENSG00000103423|ENST00000573120|Transcript|upstream_gene_variant||||2581|DNAJA3|retained_intron|||||||,-|ENSG00000103423|ENST00000574895|Transcript|upstream_gene_variant||||2412|DNAJA3|protein_coding|||||||,-|ENSG00000103426|ENST00000575334|Transcript|upstream_gene_variant||||2972|CORO7-PAM16|nonsense_mediated_decay|||||||,-|ENSG00000103423|ENST00000355296|Transcript|upstream_gene_variant||||2393|DNAJA3|protein_coding|||||||,-|ENSG00000103423|ENST00000431375|Transcript|upstream_gene_variant||||2398|DNAJA3|protein_coding|||||||,-|ENSG00000262246|ENST00000572140|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CORO7|processed_transcript|||||||;GR=-0.274;PH=-0.902;PS=0.03;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-189.1,-16.51,0:3:99:57:57 0/0:0,-16.49,-203.6:3:99:58:0 16 5193806 . AT - 2937 PASS Source=Platypus;CSQ=-|ENSG00000267070|ENST00000589323|Transcript|downstream_gene_variant||||1210|RP11-10K17.6|lincRNA|YES||||||;GR=-0.859;PH=-0.259;PS=0;SD=0.940152 GT:GL:GOF:GQ:NR:NV 1/1:-186.9,-15.35,0:2:99:53:53 1/1:-192.5,-15.35,0:0:99:54:54 16 10884461 . T C 1291 PASS Source=Platypus;CSQ=C|ENSG00000166676|ENST00000572980|Transcript|intron_variant&non_coding_transcript_variant|||||TVP23A|processed_transcript|||||||,C|ENSG00000166676|ENST00000575135|Transcript|intron_variant&NMD_transcript_variant|||||TVP23A|nonsense_mediated_decay|||||||,C|ENSG00000166676|ENST00000570692|Transcript|intron_variant&non_coding_transcript_variant|||||TVP23A|processed_transcript|||||||,C|ENSG00000166676|ENST00000299866|Transcript|intron_variant|||||TVP23A|protein_coding|YES||||||,C|ENSG00000166676|ENST00000573857|Transcript|intron_variant&non_coding_transcript_variant|||||TVP23A|processed_transcript|||||||,C|ENSG00000166676|ENST00000573360|Transcript|intron_variant&NMD_transcript_variant|||||TVP23A|nonsense_mediated_decay|||||||,C|ENSG00000166676|ENST00000456096|Transcript|intron_variant&NMD_transcript_variant|||||TVP23A|nonsense_mediated_decay|||||||;GR=0.149;PH=0.166;PS=0.09;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-18.36,-300:2:99:64:0 1/0:-82.26,0,-126.56:2:99:50:16 16 12567265 . CTGC - 2034 PASS Source=Platypus;CSQ=-|ENSG00000048471|ENST00000564791|Transcript|intron_variant&feature_truncation|||||SNX29|protein_coding|||||||,-|ENSG00000048471|ENST00000566228|Transcript|intron_variant&feature_truncation|||||SNX29|protein_coding|YES||||||,-|ENSG00000048471|ENST00000323433|Transcript|intron_variant&feature_truncation|||||SNX29|protein_coding|||||||,-|ENSG00000048471|ENST00000306030|Transcript|intron_variant&feature_truncation|||||SNX29|protein_coding|||||||;GR=3.23;PH=2.102;PS=0.012 GT:GL:GOF:GQ:NR:NV ./.:0,0,0:0:0:0:0 0/1:-5.79,0,-14.39:63:58:7:2 16 12628233 . C T 2787 PASS Source=Platypus;CSQ=T|ENSG00000048471|ENST00000566228|Transcript|intron_variant|||||SNX29|protein_coding|YES||||||,T|ENSG00000048471|ENST00000306030|Transcript|intron_variant|||||SNX29|protein_coding|||||||;GR=1.36;PH=0.564;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-221.9,-17.76,0:4:99:64:62 1/1:-151.55,-24.99,0:1:99:43:43 16 13058636 . C T 149 PASS Source=Platypus;CSQ=T|ENSG00000237515|ENST00000558583|Transcript|intron_variant|||||SHISA9|protein_coding|||||||,T|ENSG00000237515|ENST00000424107|Transcript|intron_variant|||||SHISA9|protein_coding|YES||||||,T||ENSR00001503714|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.17;PH=0.009;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-8.8,-105.7:103:88:40:6 0/1:-12.12,0,-69.92:154:99:20:3 16 14279269 . A G 1987 PASS Source=Platypus;CSQ=G|ENSG00000186260|ENST00000575768|Transcript|intron_variant&non_coding_transcript_variant|||||MKL2|processed_transcript|||||||,G|ENSG00000186260|ENST00000572567|Transcript|upstream_gene_variant||||1305|MKL2|protein_coding|||||||,G|ENSG00000186260|ENST00000318282|Transcript|intron_variant|||||MKL2|protein_coding|YES||||||,G|ENSG00000186260|ENST00000341243|Transcript|upstream_gene_variant||||1503|MKL2|protein_coding|||||||,G|ENSG00000186260|ENST00000571589|Transcript|intron_variant|||||MKL2|protein_coding|||||||,G|ENSG00000186260|ENST00000574998|Transcript|intron_variant|||||MKL2|protein_coding|||||||,G|ENSG00000186260|ENST00000574045|Transcript|intron_variant|||||MKL2|protein_coding|||||||;GR=-1.51;PH=-0.362;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-75.34,0,-100.44:4:99:58:26 0/0:0,-19.87,-246.6:0:99:67:0 16 16246827 . CACT - 2123 PASS Source=Platypus;CSQ=-|ENSG00000091262|ENST00000205557|Transcript|intron_variant&feature_truncation|||||ABCC6|protein_coding|YES||||||,-|ENSG00000091262|ENST00000456970|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ABCC6|nonsense_mediated_decay|||||||,-|ENSG00000091262|ENST00000576204|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ABCC6|retained_intron|||||||;GR=0.225;PH=0.3;PS=0.005;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-247.3,-20.47,0:2:99:71:71 1/1:-195.9,-16.23,0:2:99:56:56 16 18251389 . T C 2250 PASS Source=Platypus;CSQ=C|ENSG00000260242|ENST00000563866|Transcript|intron_variant&non_coding_transcript_variant|||||CTA-481E9.3|lincRNA|YES||||||;GR=-2.61;PH=-1.331;PS=0.002;REPMASK=SINE;SD=0.99343 GT:GL:GOF:GQ:NR:NV 0/1:-51.5,0,-68.8:4:99:45:21 1/1:-173.7,-14.45,0:3:99:49:49 16 21083405 . A G 973 PASS Source=Platypus;CSQ=G|ENSG00000158486|ENST00000261383|Transcript|intron_variant|||||DNAH3|protein_coding|YES||||||,G|ENSG00000158486|ENST00000415178|Transcript|intron_variant|||||DNAH3|protein_coding|||||||;GR=2.97;PH=1.592;PS=0.003;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/0:-53.5,0,-89.5:3:99:50:19 1/0:-125.61,0,-75.31:1:99:63:37 16 29310392 . TGT - 2400 PASS Source=Platypus;CSQ=-|ENSG00000198106|ENST00000398878|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SNX29P2|lincRNA|YES||||||,-|ENSG00000198106|ENST00000604430|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SNX29P2|lincRNA|||||||;REPMASK=Simple_repeat;SD=0.974878 GT:GL:GOF:GQ:NR:NV 0/0:0,-1.71,-167.14:52:17:73:0 0/1:-35.29,0,-48.29:20:99:47:18 16 31495991 . C T 1852 PASS Source=Platypus;CSQ=T|ENSG00000260740|ENST00000565137|Transcript|downstream_gene_variant||||2700|AC026471.6|antisense|YES||||||,T|ENSG00000140688|ENST00000568491|Transcript|downstream_gene_variant||||4824|C16orf58|retained_intron|||||||,T|ENSG00000140675|ENST00000567051|Transcript|upstream_gene_variant||||4819|SLC5A2|processed_transcript|||||||,T|ENSG00000140688|ENST00000327237|Transcript|downstream_gene_variant||||4819|C16orf58|protein_coding|YES||||||,T|ENSG00000140675|ENST00000565446|Transcript|upstream_gene_variant||||77|SLC5A2|retained_intron|||||||,T|ENSG00000140675|ENST00000562006|Transcript|splice_region_variant&intron_variant&non_coding_transcript_variant|||||SLC5A2|retained_intron|||||||,T|ENSG00000140675|ENST00000564197|Transcript|upstream_gene_variant||||4819|SLC5A2|processed_transcript|||||||,T|ENSG00000140675|ENST00000568188|Transcript|upstream_gene_variant||||3350|SLC5A2|retained_intron|||||||,T|ENSG00000140675|ENST00000568891|Transcript|upstream_gene_variant||||3540|SLC5A2|retained_intron|||||||,T|ENSG00000140675|ENST00000569576|Transcript|splice_region_variant&intron_variant|||||SLC5A2|protein_coding|||||||,T|ENSG00000140675|ENST00000419665|Transcript|splice_region_variant&intron_variant&NMD_transcript_variant|||||SLC5A2|nonsense_mediated_decay|||||||,T|ENSG00000140675|ENST00000330498|Transcript|splice_region_variant&intron_variant|||||SLC5A2|protein_coding|YES||||||,T|ENSG00000140688|ENST00000570164|Transcript|downstream_gene_variant||||4801|C16orf58|protein_coding|||||||,T||ENSR00000506610|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.692;PH=0.321;PS=0.798;WGS500=2;ExAC=1/121410 GT:GL:GOF:GQ:NR:NV 0/1:-105.24,0,-74.34:5:99:59:34 0/1:-84.65,0,-59.05:4:99:50:30 16 32326621 . G A 1694 PASS Source=Platypus;CSQ=A|ENSG00000261127|ENST00000568567|Transcript|upstream_gene_variant||||4745|RP11-17M15.2|processed_transcript|YES||||||;SD=0.990959 GT:GL:GOF:GQ:NR:NV 0/0:0,-11.05,-134.9:3:99:39:0 1/0:-53.86,0,-63.66:1:99:40:19 16 33221454 . GAAG - 429 PASS Source=Platypus;CSQ=-|ENSG00000260827|ENST00000563960|Transcript|upstream_gene_variant||||3671|RP11-1437A8.4|lincRNA|YES||||||,-|ENSG00000205457|ENST00000398667|Transcript|intron_variant&feature_truncation|||||TP53TG3C|protein_coding|||||||,-|ENSG00000261507|ENST00000569199|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-1437A8.6|lincRNA|YES||||||;REPMASK=LINE;SD=0.997448 GT:GL:GOF:GQ:NR:NV 1/1:-31.4,-2.41,0:0:24:9:9 1/1:-110.1,-8.73,0:1:87:30:30 16 35194665 . A G 457 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;REPMASK=Satellite GT:GL:GOF:GQ:NR:NV 0/0:0,-7.53,-59.8:1:75:29:0 0/1:-73.74,0,-41.24:5:99:62:27 16 47152398 . T C 575 PASS Source=Platypus;CSQ=C|ENSG00000171208|ENST00000562435|Transcript|intron_variant|||||NETO2|protein_coding|YES||||||,C|ENSG00000171208|ENST00000303155|Transcript|intron_variant|||||NETO2|protein_coding|||||||,C|ENSG00000171208|ENST00000563078|Transcript|intron_variant|||||NETO2|protein_coding|||||||,C|ENSG00000238834|ENST00000458876|Transcript|downstream_gene_variant||||2432|snoU13|snoRNA|YES||||||,C|ENSG00000171208|ENST00000562559|Transcript|intron_variant|||||NETO2|protein_coding|||||||;GR=0.554;PH=0.454;PS=0.018;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-94.8,0,-76.5:12:99:60:32 0/0:0,-13.85,-176.9:12:99:47:0 16 50152652 . A G 426 PASS Source=Platypus;CSQ=G|ENSG00000260381|ENST00000566770|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-429P3.5|antisense|YES||||||;GR=0.109;PH=0.156;PS=0.411;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-40.08,0,-80.68:3:99:45:17 0/1:-84.19,0,-71.99:3:99:56:30 16 51144144 . CCAG - 1385 PASS Source=Platypus;CSQ=-|ENSG00000261282|ENST00000563903|Transcript|downstream_gene_variant||||2212|SOD1P2|processed_pseudogene|YES||||||;GR=2.21;PH=0.661;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-74.24,0,-99.14:2:99:59:25 1/1:-191.5,-15.65,0:2:99:53:53 16 53239128 . T C 1089 PASS Source=Platypus;CSQ=C|ENSG00000177200|ENST00000566029|Transcript|intron_variant|||||CHD9|protein_coding|YES||||||,C|ENSG00000177200|ENST00000569794|Transcript|upstream_gene_variant||||2816|CHD9|processed_transcript|||||||,C|ENSG00000177200|ENST00000564845|Transcript|intron_variant|||||CHD9|protein_coding|||||||,C|ENSG00000177200|ENST00000562791|Transcript|upstream_gene_variant||||4564|CHD9|processed_transcript|||||||,C|ENSG00000177200|ENST00000564255|Transcript|intron_variant&non_coding_transcript_variant|||||CHD9|retained_intron|||||||,C|ENSG00000177200|ENST00000565442|Transcript|upstream_gene_variant||||3235|CHD9|protein_coding|||||||,C|ENSG00000177200|ENST00000565832|Transcript|intron_variant|||||CHD9|protein_coding|||||||,C|ENSG00000177200|ENST00000565803|Transcript|upstream_gene_variant||||2773|CHD9|protein_coding|||||||,C|ENSG00000177200|ENST00000447540|Transcript|intron_variant|||||CHD9|protein_coding|||||||,C|ENSG00000177200|ENST00000398510|Transcript|intron_variant|||||CHD9|protein_coding|||||||;GR=-0.613;PH=-0.141;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-73.87,0,-81.47:4:99:56:28 1/0:-51.76,0,-77.86:3:99:46:20 16 53264598 . AT - 616 PASS Source=Platypus;CSQ=-|ENSG00000177200|ENST00000566029|Transcript|intron_variant&feature_truncation|||||CHD9|protein_coding|YES||||||,-|ENSG00000177200|ENST00000564845|Transcript|intron_variant&feature_truncation|||||CHD9|protein_coding|||||||,-|ENSG00000177200|ENST00000219084|Transcript|upstream_gene_variant||||4450|CHD9|retained_intron|||||||,-|ENSG00000177200|ENST00000562791|Transcript|downstream_gene_variant||||4283|CHD9|processed_transcript|||||||,-|ENSG00000177200|ENST00000564255|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CHD9|retained_intron|||||||,-|ENSG00000177200|ENST00000565803|Transcript|intron_variant&feature_truncation|||||CHD9|protein_coding|||||||,-|ENSG00000177200|ENST00000569225|Transcript|upstream_gene_variant||||4450|CHD9|retained_intron|||||||,-|ENSG00000177200|ENST00000447540|Transcript|intron_variant&feature_truncation|||||CHD9|protein_coding|||||||,-|ENSG00000177200|ENST00000398510|Transcript|intron_variant&feature_truncation|||||CHD9|protein_coding|||||||;GR=1.34;PH=0.869;PS=0.011;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.42,-159.1:3:99:47:0 0/1:-41.58,0,-95.28:4:99:47:16 16 54968864 . TG - 2683 PASS Source=Platypus;CSQ=-|ENSG00000176842|ENST00000558597|Transcript|downstream_gene_variant||||883|IRX5|protein_coding|||||||,-|ENSG00000259725|ENST00000558156|Transcript|downstream_gene_variant||||3078|CTD-3032H12.1|lincRNA|||||||,-|ENSG00000259725|ENST00000559802|Transcript|downstream_gene_variant||||2833|CTD-3032H12.1|lincRNA|YES||||||,-|ENSG00000176842|ENST00000320990|Transcript|downstream_gene_variant||||467|IRX5|protein_coding|||||||,-|ENSG00000176842|ENST00000560154|Transcript|downstream_gene_variant||||992|IRX5|protein_coding|||||||,-|ENSG00000176842|ENST00000394636|Transcript|downstream_gene_variant||||467|IRX5|protein_coding|YES||||||,-|ENSG00000259711|ENST00000560487|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|40-41||||CTD-3032H12.2|lincRNA|YES||||||,-||ENSR00000507764|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.81;PH=0.376;PS=0.709 GT:GL:GOF:GQ:NR:NV 1/1:-176.3,-14.15,0:4:99:50:50 0/1:-86,0,-66.1:2:99:55:31 16 55138231 . GCC - 1504 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.612;PH=-0.116;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-21.07,-255.9:2:99:74:0 0/1:-88.36,0,-96.66:15:99:62:29 16 55273626 . G A 2092 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-2.3;PH=-0.53;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.87,-182.3:2:99:57:0 0/1:-44.96,0,-60.46:4:99:46:22 16 56050936 . AG - 2360 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.94;PH=1.584;PS=0.035;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-75.99,-11.46,0:20:99:58:44 1/1:-68,-7.44,0:16:74:46:33 16 62334587 . TG - 2666 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.73;PH=0.15;PS=0.023;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-110.4,-9.33,0:6:93:33:33 1/1:-219.4,-18.06,0:0:99:62:62 16 64171292 . GGAG - 1316 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.85;PH=-0.471;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-99.3,-7.83,0:55:78:26:26 1/1:-121.5,-10.24,0:19:99:35:35 16 66919133 . G A 1484 PASS Source=Platypus;CSQ=A|ENSG00000172840|ENST00000568398|Transcript|downstream_gene_variant||||864|PDP2|protein_coding|||||||,A|ENSG00000261088|ENST00000561811|Transcript|upstream_gene_variant||||3939|RP11-61A14.3|lincRNA|||||||,A|ENSG00000172840|ENST00000566543|Transcript|downstream_gene_variant||||491|PDP2|protein_coding|||||||,A|ENSG00000172840|ENST00000561704|Transcript|downstream_gene_variant||||636|PDP2|protein_coding|||||||,A|ENSG00000172840|ENST00000568720|Transcript|intron_variant&non_coding_transcript_variant|||||PDP2|processed_transcript|||||||,A|ENSG00000172840|ENST00000566776|Transcript|downstream_gene_variant||||219|PDP2|protein_coding|||||||,A|ENSG00000261088|ENST00000563086|Transcript|upstream_gene_variant||||3961|RP11-61A14.3|lincRNA|YES||||||,A|ENSG00000261705|ENST00000561475|Transcript|upstream_gene_variant||||2785|RP11-61A14.2|lincRNA|YES||||||,A|ENSG00000172840|ENST00000566805|Transcript|intron_variant&NMD_transcript_variant|||||PDP2|nonsense_mediated_decay|||||||,A|ENSG00000172840|ENST00000568869|Transcript|downstream_gene_variant||||481|PDP2|protein_coding|||||||,A|ENSG00000172840|ENST00000311765|Transcript|missense_variant|1280|316|E/K||PDP2|protein_coding|YES|deleterious(0)|probably_damaging(1)||||;GR=5.92;PH=2.812;PS=0.973;UK10K=1/7562;WGS500=2;ExAC=6/121412 GT:GL:GOF:GQ:NR:NV 1/0:-81.61,0,-67.71:3:99:51:27 1/0:-71.45,0,-80.55:2:99:53:26 16 67208979 . G T 1242 PASS Source=Platypus;CSQ=T|ENSG00000196123|ENST00000563831|Transcript|downstream_gene_variant||||1695|KIAA0895L|processed_transcript|||||||,T|ENSG00000140939|ENST00000568199|Transcript|downstream_gene_variant||||2073|NOL3|processed_transcript|||||||,T|ENSG00000140939|ENST00000563439|Transcript|downstream_gene_variant||||335|NOL3|protein_coding|||||||,T|ENSG00000196123|ENST00000563918|Transcript|downstream_gene_variant||||1574|KIAA0895L|processed_transcript|||||||,T|ENSG00000140939|ENST00000565645|Transcript|downstream_gene_variant||||1147|NOL3|processed_transcript|||||||,T|ENSG00000196123|ENST00000568165|Transcript|downstream_gene_variant||||4405|KIAA0895L|retained_intron|||||||,T|ENSG00000196123|ENST00000290881|Transcript|downstream_gene_variant||||528|KIAA0895L|protein_coding|YES||||||,T|ENSG00000196123|ENST00000561621|Transcript|downstream_gene_variant||||528|KIAA0895L|protein_coding|||||||,T|ENSG00000140939|ENST00000432069|Transcript|3_prime_UTR_variant|1221||||NOL3|protein_coding|||||||,T|ENSG00000196123|ENST00000569349|Transcript|downstream_gene_variant||||528|KIAA0895L|nonsense_mediated_decay|||||||,T|ENSG00000196123|ENST00000570009|Transcript|downstream_gene_variant||||3369|KIAA0895L|processed_transcript|||||||,T|ENSG00000140939|ENST00000568086|Transcript|downstream_gene_variant||||3420|NOL3|retained_intron|||||||,T|ENSG00000140939|ENST00000568503|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|906||||NOL3|retained_intron|||||||,T|ENSG00000140939|ENST00000564053|Transcript|3_prime_UTR_variant|1183||||NOL3|protein_coding|||||||,T|ENSG00000196123|ENST00000568563|Transcript|downstream_gene_variant||||528|KIAA0895L|protein_coding|||||||,T|ENSG00000196123|ENST00000561679|Transcript|downstream_gene_variant||||528|KIAA0895L|retained_intron|||||||,T|ENSG00000196123|ENST00000564423|Transcript|downstream_gene_variant||||4354|KIAA0895L|processed_transcript|||||||,T|ENSG00000140939|ENST00000564860|Transcript|missense_variant|133|45|G/V||NOL3|protein_coding|||unknown(0)||||,T|ENSG00000140939|ENST00000268605|Transcript|3_prime_UTR_variant|737||||NOL3|protein_coding|||||||,T|ENSG00000140939|ENST00000563258|Transcript|3_prime_UTR_variant|417||||NOL3|protein_coding|||||||,T|ENSG00000140939|ENST00000568146|Transcript|synonymous_variant|692|213|R||NOL3|protein_coding|YES||||||,T|ENSG00000196123|ENST00000564835|Transcript|downstream_gene_variant||||4042|KIAA0895L|retained_intron|||||||,T|ENSG00000140939|ENST00000565560|Transcript|downstream_gene_variant||||228|NOL3|protein_coding|||||||,T|ENSG00000196123|ENST00000563902|Transcript|downstream_gene_variant||||1654|KIAA0895L|protein_coding|||||||,T|ENSG00000140939|ENST00000564992|Transcript|downstream_gene_variant||||132|NOL3|protein_coding|||||||,T|ENSG00000140939|ENST00000566871|Transcript|synonymous_variant|629|210|R||NOL3|protein_coding|||||||,T|ENSG00000196123|ENST00000562514|Transcript|downstream_gene_variant||||526|KIAA0895L|processed_transcript|||||||;GR=-4.33;PH=-0.467;PS=0;WGS500=2;ExAC=3/120962 GT:GL:GOF:GQ:NR:NV 0/1:-56.56,0,-57.46:3:99:42:21 0/1:-72.36,0,-41.06:2:99:43:26 16 71579641 . TT - 2973 PASS Source=Platypus;CSQ=-|ENSG00000260015|ENST00000568523|Transcript|upstream_gene_variant||||3913|RP11-510M2.5|sense_intronic|YES||||||,-|ENSG00000157429|ENST00000564225|Transcript|intron_variant&feature_truncation|||||ZNF19|protein_coding|||||||,-|ENSG00000157429|ENST00000568446|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZNF19|processed_transcript|||||||,-|ENSG00000157429|ENST00000566202|Transcript|intron_variant&feature_truncation|||||ZNF19|protein_coding|||||||;GR=0.53;PH=0.433;PS=0.012;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 2/2:-1,-1,-1:6:69:39,39:22,22 1/2:-1,-1,-1:4:99:41,41:19,19 16 75937345 . T C 2401 PASS Source=Platypus;CSQ=C||ENSR00001506563|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=2.63;PH=1.452;PS=0.01;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-169.2,-15,0:3:99:58:55 1/1:-118.4,-11.41,0:4:99:43:43 16 81212260 . TG - 1950 PASS Source=Platypus;CSQ=-|ENSG00000166473|ENST00000531391|Transcript|intron_variant&feature_truncation|||||PKD1L2|protein_coding|||||||,-|ENSG00000166473|ENST00000526632|Transcript|intron_variant&feature_truncation|||||PKD1L2|protein_coding|||||||,-|ENSG00000166473|ENST00000525539|Transcript|intron_variant&feature_truncation|||||PKD1L2|polymorphic_pseudogene|||||||,-|ENSG00000166473|ENST00000529791|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PKD1L2|processed_transcript|||||||,-|ENSG00000166473|ENST00000299598|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PKD1L2|retained_intron|||||||,-|ENSG00000166473|ENST00000527937|Transcript|intron_variant&feature_truncation|||||PKD1L2|protein_coding|YES||||||,-|ENSG00000166473|ENST00000533478|Transcript|intron_variant&feature_truncation|||||PKD1L2|polymorphic_pseudogene|||||||,-|ENSG00000166473|ENST00000337114|Transcript|intron_variant&feature_truncation|||||PKD1L2|protein_coding|||||||;GR=0.384;PH=-0.306;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-163.5,-13.25,0:1:99:49:47 0/1:-65.45,0,-77.15:1:99:45:22 16 85130495 . A G 2831 PASS Source=Platypus;CSQ=G|ENSG00000153789|ENST00000539556|Transcript|downstream_gene_variant||||1470|FAM92B|protein_coding|YES||||||,G|ENSG00000135709|ENST00000258180|Transcript|downstream_gene_variant||||2669|KIAA0513|protein_coding|||||||,G|ENSG00000135709|ENST00000566428|Transcript|downstream_gene_variant||||2659|KIAA0513|protein_coding|YES||||||;GR=-0.431;PH=-1.022;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-73.27,0,-75.27:11:99:51:24 1/1:-207.2,-16.65,0:28:99:57:57 16 85324325 . A G 344 PASS Source=Platypus;CSQ=G|ENSG00000179219|ENST00000366314|Transcript|downstream_gene_variant||||4756|LINC00311|lincRNA|YES||||||;GR=0.311;PH=0.068;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-212.7,-17.16,0:1:99:59:59 1/1:-183.7,-14.45,0:1:99:49:49 16 90036263 . C T 585 PASS Source=Platypus;CSQ=T|ENSG00000140995|ENST00000563805|Transcript|downstream_gene_variant||||3512|DEF8|retained_intron|||||||,T|ENSG00000140995|ENST00000561959|Transcript|downstream_gene_variant||||3949|DEF8|protein_coding|||||||,T|ENSG00000223959|ENST00000418696|Transcript|upstream_gene_variant||||2731|AFG3L1P|processed_transcript|||||||,T|ENSG00000140995|ENST00000567874|Transcript|downstream_gene_variant||||3687|DEF8|protein_coding|||||||,T|ENSG00000223959|ENST00000429663|Transcript|upstream_gene_variant||||2731|AFG3L1P|processed_transcript|||||||,T|ENSG00000140995|ENST00000564379|Transcript|downstream_gene_variant||||2222|DEF8|retained_intron|||||||,T|ENSG00000140995|ENST00000563594|Transcript|downstream_gene_variant||||1795|DEF8|protein_coding|||||||,T|ENSG00000140995|ENST00000569453|Transcript|downstream_gene_variant||||3789|DEF8|protein_coding|||||||,T|ENSG00000223959|ENST00000457926|Transcript|upstream_gene_variant||||2738|AFG3L1P|processed_transcript|||||||,T|ENSG00000223959|ENST00000423742|Transcript|upstream_gene_variant||||2739|AFG3L1P|retained_intron|||||||,T|ENSG00000177946|ENST00000314994|Transcript|3_prime_UTR_variant|2680||||CENPBD1|protein_coding|YES||||||,T|ENSG00000140995|ENST00000268676|Transcript|downstream_gene_variant||||1795|DEF8|protein_coding|YES||||||,T|ENSG00000177946|ENST00000567035|Transcript|downstream_gene_variant||||193|CENPBD1|processed_transcript|||||||,T|ENSG00000223959|ENST00000421164|Transcript|upstream_gene_variant||||2793|AFG3L1P|retained_intron|||||||,T|ENSG00000261317|ENST00000565150|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|65||||RP11-566K11.5|antisense|YES||||||,T|ENSG00000223959|ENST00000431757|Transcript|upstream_gene_variant||||2731|AFG3L1P|processed_transcript|||||||,T|ENSG00000223959|ENST00000450026|Transcript|upstream_gene_variant||||2734|AFG3L1P|retained_intron|||||||,T|ENSG00000140995|ENST00000570182|Transcript|downstream_gene_variant||||1796|DEF8|protein_coding|||||||,T|ENSG00000223959|ENST00000437774|Transcript|upstream_gene_variant||||2762|AFG3L1P|processed_transcript|||||||,T|ENSG00000140995|ENST00000562163|Transcript|downstream_gene_variant||||3811|DEF8|processed_transcript|||||||,T|ENSG00000223959|ENST00000436447|Transcript|upstream_gene_variant||||2738|AFG3L1P|processed_transcript|||||||,T|ENSG00000140995|ENST00000563795|Transcript|downstream_gene_variant||||3549|DEF8|protein_coding|||||||,T|ENSG00000223959|ENST00000557444|Transcript|upstream_gene_variant||||2776|AFG3L1P|unitary_pseudogene|||||||;GR=0.868;PH=0.57;PS=0.004 GT:GL:GOF:GQ:NR:NV 0/0:0,-11.14,-167.2:1:99:38:0 0/1:-21.17,0,-76.07:3:99:26:5 17 536439 . ATC - 1692 PASS Source=Platypus;CSQ=-|ENSG00000141252|ENST00000576149|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||VPS53|processed_transcript|||||||,-|ENSG00000141252|ENST00000446250|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|||||||,-|ENSG00000141252|ENST00000571805|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|||||||,-|ENSG00000141252|ENST00000389040|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||VPS53|nonsense_mediated_decay|||||||,-|ENSG00000141252|ENST00000574029|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|||||||,-|ENSG00000141252|ENST00000437048|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|YES||||||,-|ENSG00000141252|ENST00000573028|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||VPS53|nonsense_mediated_decay|||||||,-|ENSG00000141252|ENST00000291074|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|||||||,-|ENSG00000141252|ENST00000572334|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||VPS53|processed_transcript|||||||,-|ENSG00000141252|ENST00000401468|Transcript|intron_variant&feature_truncation|||||VPS53|protein_coding|||||||,-|ENSG00000141252|ENST00000570650|Transcript|upstream_gene_variant||||4968|VPS53|protein_coding|||||||;GR=0.158;PH=0.175;PS=0.012 GT:GL:GOF:GQ:NR:NV 0/1:-152.55,0,-126.45:2:99:56:23 1/1:-288.2,-12.64,0:0:99:46:38 17 3512437 . C T 2455 PASS Source=Platypus;CSQ=T|ENSG00000262304|ENST00000572705|Transcript|intron_variant|||||SHPK|protein_coding|YES||||||,T|ENSG00000197417|ENST00000225519|Transcript|3_prime_UTR_variant|2957||||SHPK|protein_coding|YES||||||,T|ENSG00000262304|ENST00000572919|Transcript|intron_variant&NMD_transcript_variant|||||SHPK|nonsense_mediated_decay|||||||;GR=0.457;PH=0.552;PS=0.011;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-56.2,0,-72.4:4:99:43:18 1/0:-75.64,0,-96.04:3:99:60:27 17 5840214 . T C 2768 PASS Source=Platypus;CSQ=C|ENSG00000179314|ENST00000573619|Transcript|intron_variant|||||WSCD1|protein_coding|||||||;GR=-2.06;PH=-0.557;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-161.6,-13.25,0:2:99:48:48 1/1:-147.9,-12.43,0:3:99:43:43 17 6483602 . A G 2935 PASS Source=Platypus;CSQ=G|ENSG00000198920|ENST00000542606|Transcript|intron_variant|||||KIAA0753|protein_coding|||||||,G|ENSG00000198920|ENST00000589033|Transcript|intron_variant|||||KIAA0753|protein_coding|||||||,G|ENSG00000198920|ENST00000361413|Transcript|intron_variant|||||KIAA0753|protein_coding|YES||||||,G|ENSG00000198920|ENST00000572370|Transcript|intron_variant|||||KIAA0753|protein_coding|||||||,G|ENSG00000198920|ENST00000570790|Transcript|intron_variant&NMD_transcript_variant|||||KIAA0753|nonsense_mediated_decay|||||||,G|ENSG00000198920|ENST00000542826|Transcript|intron_variant&NMD_transcript_variant|||||KIAA0753|nonsense_mediated_decay|||||||,G|ENSG00000198920|ENST00000576281|Transcript|intron_variant|||||KIAA0753|protein_coding|||||||;GR=0.148;PH=0.047;PS=0.1;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-50.55,0,-139.15:2:99:65:20 1/0:-15.84,0,-163.54:3:99:57:9 17 8155021 . A G 1767 PASS Source=Platypus;CSQ=G|ENSG00000178921|ENST00000580356|Transcript|intron_variant&NMD_transcript_variant|||||PFAS|nonsense_mediated_decay|||||||,G|ENSG00000178971|ENST00000581671|Transcript|upstream_gene_variant||||3662|CTC1|processed_transcript|||||||,G|ENSG00000178921|ENST00000584044|Transcript|intron_variant|||||PFAS|protein_coding|||||||,G|ENSG00000178921|ENST00000314666|Transcript|intron_variant|||||PFAS|protein_coding|YES||||||,G|ENSG00000178971|ENST00000449476|Transcript|upstream_gene_variant||||3661|CTC1|nonsense_mediated_decay|||||||,G|ENSG00000178921|ENST00000585183|Transcript|intron_variant|||||PFAS|protein_coding|||||||,G|ENSG00000178921|ENST00000545834|Transcript|intron_variant|||||PFAS|protein_coding|||||||,G|ENSG00000178971|ENST00000315684|Transcript|upstream_gene_variant||||3659|CTC1|protein_coding|YES||||||,G|ENSG00000178921|ENST00000581242|Transcript|intron_variant|||||PFAS|protein_coding|||||||;GR=-0.865;PH=-1.223;PS=0.006;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.95,-183.3:4:99:58:0 0/1:-76.45,0,-69.25:1:99:50:26 17 11836273 . AGAG - 311 PASS Source=Platypus;CSQ=-|ENSG00000007174|ENST00000454412|Transcript|intron_variant&feature_truncation|||||DNAH9|protein_coding|||||||,-|ENSG00000007174|ENST00000608377|Transcript|intron_variant&feature_truncation|||||DNAH9|protein_coding|||||||,-|ENSG00000007174|ENST00000396001|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||DNAH9|processed_transcript|||||||,-|ENSG00000007174|ENST00000262442|Transcript|intron_variant&feature_truncation|||||DNAH9|protein_coding|YES||||||;GR=-1.71;PH=-0.741;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-58.85,0,-83.95:2:99:46:21 1/0:-114.55,0,-74.83:1:99:57:31 17 13641208 . GT - 2293 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-6.03;PH=-2.14;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-86.44,0,-87.44:3:99:58:29 1/1:-204.4,-17.06,0:2:99:60:60 17 14801661 . GAA - 900 PASS Source=Platypus;CSQ=-|ENSG00000238212|ENST00000445035|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AC005863.2|lincRNA|YES||||||;GR=-0.965;PH=-1.706;PS=0;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/0:0,-3.61,-67.5:3:36:14:0 1/0:-79.21,0,-97.31:3:99:42:18 17 16025541 . AC - 2229 PASS Source=Platypus;CSQ=-|ENSG00000141027|ENST00000582357|Transcript|downstream_gene_variant||||3879|NCOR1|protein_coding|||||||,-|ENSG00000141027|ENST00000395848|Transcript|intron_variant&feature_truncation|||||NCOR1|protein_coding|||||||,-|ENSG00000141027|ENST00000583226|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NCOR1|processed_transcript|||||||,-|ENSG00000141027|ENST00000395851|Transcript|intron_variant&feature_truncation|||||NCOR1|protein_coding|||||||,-|ENSG00000141027|ENST00000460276|Transcript|downstream_gene_variant||||3904|NCOR1|nonsense_mediated_decay|||||||,-|ENSG00000141027|ENST00000436828|Transcript|downstream_gene_variant||||3904|NCOR1|protein_coding|||||||,-|ENSG00000141027|ENST00000411510|Transcript|downstream_gene_variant||||3854|NCOR1|protein_coding|||||||,-|ENSG00000141027|ENST00000268712|Transcript|intron_variant&feature_truncation|||||NCOR1|protein_coding|YES||||||;GR=-0.941;PH=-0.219;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-187.7,-15.63,0:24:99:57:57 1/0:-95.45,0,-53.65:20:99:47:29 17 17535173 . T C 1205 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.303;PH=0.355;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-10.21,-116.6:2:99:35:0 1/0:-72.2,0,-45.6:13:99:44:25 17 21701546 . AA - 855 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.83;PH=0.628;PS=0.007;SD=0.947913 GT:GL:GOF:GQ:NR:NV 1/0:-80.2,0,-81.1:2:99:58:30 1/0:-80.06,0,-42.06:1:99:40:24 17 21713588 . A G 1284 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.987;PH=0.698;PS=0.001;SD=0.946395 GT:GL:GOF:GQ:NR:NV 1/0:-56.85,0,-74.05:1:99:47:21 0/0:0,-16.83,-200.6:1:99:60:0 17 26083040 . T C 1031 PASS Source=Platypus;CSQ=C|ENSG00000007171|ENST00000313735|Transcript|downstream_gene_variant||||752|NOS2|protein_coding|YES||||||,C|ENSG00000266786|ENST00000580112|Transcript|downstream_gene_variant||||1060|RP1-66C13.3|unprocessed_pseudogene|YES||||||;GR=-2.14;PH=-0.639;PS=0;SD=0.929749 GT:GL:GOF:GQ:NR:NV 1/0:-108.02,0,-97.22:14:99:61:30 1/0:-70.72,0,-81.72:8:99:45:21 17 26399977 . G A 425 PASS Source=Platypus;CSQ=A|ENSG00000087095|ENST00000496808|Transcript|intron_variant&NMD_transcript_variant|||||NLK|nonsense_mediated_decay|||||||,A|ENSG00000087095|ENST00000407008|Transcript|intron_variant|||||NLK|protein_coding|YES||||||;GR=-0.834;PH=-0.19;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-3.59,0,-28.09:5:36:12:2 0/1:-16.98,0,-37.48:4:99:19:6 17 26720479 . AGG - 810 PASS Source=Platypus;CSQ=-|ENSG00000076351|ENST00000584729|Transcript|downstream_gene_variant||||1294|SLC46A1|processed_transcript|||||||,-|ENSG00000004139|ENST00000457710|Transcript|intron_variant&feature_truncation|||||SARM1|protein_coding|YES||||||,-|ENSG00000004139|ENST00000579593|Transcript|intron_variant&feature_truncation|||||SARM1|protein_coding|||||||,-|ENSG00000004139|ENST00000580711|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SARM1|retained_intron|||||||,-|ENSG00000076351|ENST00000440501|Transcript|downstream_gene_variant||||1180|SLC46A1|protein_coding|YES||||||,-|ENSG00000004139|ENST00000003834|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SARM1|retained_intron|||||||,-|ENSG00000076351|ENST00000583295|Transcript|downstream_gene_variant||||2214|SLC46A1|processed_transcript|||||||,-|ENSG00000004139|ENST00000379061|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SARM1|processed_transcript|||||||,-|ENSG00000076351|ENST00000321666|Transcript|downstream_gene_variant||||1180|SLC46A1|protein_coding|||||||,-|ENSG00000004139|ENST00000578128|Transcript|intron_variant&feature_truncation|||||SARM1|protein_coding|||||||,-|ENSG00000004139|ENST00000577870|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SARM1|retained_intron|||||||;GR=0.158;PH=0.175;PS=0.011;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-22.35,0,-53.95:4:99:39:6 1/0:-95.16,0,-51.26:15:99:50:12 17 26915991 . CAT - 1287 PASS Source=Platypus;CSQ=-|ENSG00000076382|ENST00000536674|Transcript|downstream_gene_variant||||3497|SPAG5|protein_coding|||||||,-|ENSG00000076382|ENST00000578479|Transcript|downstream_gene_variant||||2723|SPAG5|nonsense_mediated_decay|||||||,-|ENSG00000258472|ENST00000481916|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||RP11-192H23.4|nonsense_mediated_decay|||||||,-|ENSG00000258472|ENST00000531839|Transcript|intron_variant&feature_truncation|||||RP11-192H23.4|protein_coding|YES||||||,-|ENSG00000076382|ENST00000321765|Transcript|intron_variant&feature_truncation|||||SPAG5|protein_coding|YES||||||,-|ENSG00000076382|ENST00000580567|Transcript|downstream_gene_variant||||2723|SPAG5|nonsense_mediated_decay|||||||,-|ENSG00000076382|ENST00000378976|Transcript|upstream_gene_variant||||4311|SPAG5|nonsense_mediated_decay|||||||,-|ENSG00000076382|ENST00000584206|Transcript|intron_variant&feature_truncation|||||SPAG5|protein_coding|||||||,-|ENSG00000076382|ENST00000580083|Transcript|upstream_gene_variant||||2975|SPAG5|nonsense_mediated_decay|||||||;GR=0.401;PH=0.436;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-204.4,-17.44,0:1:99:60:60 1/0:-58.46,0,-68.46:2:99:44:21 17 30444784 . C T 235 PASS Source=Platypus;CSQ=T|ENSG00000263369|ENST00000580412|Transcript|upstream_gene_variant||||3643|RP11-640N20.9|processed_transcript|||||||,T|ENSG00000263369|ENST00000583895|Transcript|upstream_gene_variant||||3640|RP11-640N20.9|transcribed_unprocessed_pseudogene|YES||||||;GR=-0.692;PH=-0.315;PS=0.006;SD=0.951276 GT:GL:GOF:GQ:NR:NV 1/0:-79.35,0,-71.25:2:99:54:28 0/0:0,-14.69,-181.2:3:99:52:0 17 31916707 rs184640429 G A 2948 PASS Source=Platypus;CSQ=A|ENSG00000265125|ENST00000579975|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-31I22.3|antisense|YES||||||,A|ENSG00000108684|ENST00000359872|Transcript|intron_variant|||||ASIC2|protein_coding|||||||;GR=0.692;PH=-0.335;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-163.1,-13.75,0:1:99:49:48 0/0:0,-16.16,-196:0:99:55:0 17 33561687 . AGTA - 2545 PASS Source=Platypus;CSQ=-|ENSG00000266947|ENST00000590478|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-799D4.4|antisense|YES||||||,-|ENSG00000266947|ENST00000588697|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-799D4.4|antisense|||||||;GR=-0.298;PH=-1.12;PS=0.027;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-107.95,0,-56.75:15:99:54:34 0/0:0,-12.64,-155.7:18:99:43:0 17 35724767 rs535497357 G A 1325 PASS Source=Platypus;CSQ=A|ENSG00000132142|ENST00000416895|Transcript|intron_variant|||||ACACA|protein_coding|||||||,A|ENSG00000132142|ENST00000587545|Transcript|intron_variant&non_coding_transcript_variant|||||ACACA|processed_transcript|||||||,A|ENSG00000132142|ENST00000456561|Transcript|upstream_gene_variant||||2258|ACACA|non_stop_decay|||||||,A|ENSG00000132142|ENST00000456066|Transcript|intron_variant&NMD_transcript_variant|||||ACACA|nonsense_mediated_decay|||||||,A|ENSG00000132142|ENST00000353139|Transcript|intron_variant|||||ACACA|protein_coding|YES||||||,A|ENSG00000132142|ENST00000587653|Transcript|intron_variant&non_coding_transcript_variant|||||ACACA|processed_transcript|||||||,A|ENSG00000132142|ENST00000451642|Transcript|intron_variant|||||ACACA|protein_coding|||||||,A|ENSG00000132142|ENST00000413318|Transcript|intron_variant|||||ACACA|protein_coding|||||||;GR=-1.13;PH=-4.494;PS=0;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.85,-169.8:2:99:50:0 0/1:-51.05,0,-91.15:8:99:47:18 17 35871867 . AT - 2194 PASS Source=Platypus;CSQ=-|ENSG00000161326|ENST00000394386|Transcript|intron_variant&feature_truncation|||||DUSP14|protein_coding|||||||,-|ENSG00000161326|ENST00000394389|Transcript|intron_variant&feature_truncation|||||DUSP14|protein_coding|||||||,-|ENSG00000006114|ENST00000590102|Transcript|downstream_gene_variant||||3680|SYNRG|processed_transcript|||||||,-|ENSG00000161326|ENST00000487847|Transcript|intron_variant&feature_truncation|||||DUSP14|protein_coding|YES||||||,-|ENSG00000006114|ENST00000339208|Transcript|downstream_gene_variant||||3032|SYNRG|protein_coding|YES||||||,-|ENSG00000006114|ENST00000346661|Transcript|downstream_gene_variant||||3033|SYNRG|protein_coding|||||||;GR=-0.433;PH=-1.003;PS=0.012;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-51.96,0,-62.66:1:99:40:17 0/0:0,-14.35,-171.3:1:99:50:0 17 47596668 . AG - 1499 PASS Source=Platypus;CSQ=-|ENSG00000064300|ENST00000172229|Transcript|downstream_gene_variant||||4289|NGFR|protein_coding|YES||||||,-|ENSG00000249906|ENST00000514506|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP5-1029K10.2|antisense|YES||||||;GR=-0.846;PH=-0.299;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-77.07,0,-74.27:3:99:53:27 0/1:-59.67,0,-89.17:26:99:50:21 17 51730445 . GG - 464 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.33;PH=0.412;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/1:-149.3,-12.94,0:5:99:46:46 1/1:-179.1,-15.05,0:1:99:51:51 17 53759363 . AA - 1322 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.52;PH=0.977;PS=0.683 GT:GL:GOF:GQ:NR:NV 1/0:-95.31,0,-54.41:4:99:55:33 0/0:0,-12.64,-147.7:3:99:47:0 17 55499648 rs59928727 C T 2256 PASS Source=Platypus;CSQ=T|ENSG00000153944|ENST00000579590|Transcript|intron_variant|||||MSI2|protein_coding|||||||,T|ENSG00000153944|ENST00000284073|Transcript|intron_variant|||||MSI2|protein_coding|YES||||||,T|ENSG00000153944|ENST00000579205|Transcript|intron_variant&non_coding_transcript_variant|||||MSI2|processed_transcript|||||||,T|ENSG00000153944|ENST00000416426|Transcript|intron_variant|||||MSI2|protein_coding|||||||,T|ENSG00000153944|ENST00000582453|Transcript|intron_variant&non_coding_transcript_variant|||||MSI2|processed_transcript|||||||,T|ENSG00000153944|ENST00000579180|Transcript|intron_variant|||||MSI2|protein_coding|||||||,T|ENSG00000153944|ENST00000322684|Transcript|intron_variant|||||MSI2|protein_coding|||||||,T|ENSG00000153944|ENST00000442934|Transcript|intron_variant|||||MSI2|protein_coding|||||||;GR=0.521;PH=0.51;PS=0.016;REPMASK=SINE;1000G=0.0333466 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.63,-215:0:99:63:0 1/0:-75.85,0,-65.75:0:99:48:25 17 58190234 . A G 2552 PASS Source=Platypus;CSQ=G|ENSG00000267295|ENST00000590609|Transcript|downstream_gene_variant||||920|CTD-2319I12.3|unprocessed_pseudogene|YES||||||;GR=0.726;PH=0.596;PS=0.26;REPMASK=Low_complexity;SD=0.99738 GT:GL:GOF:GQ:NR:NV 0/0:0,-32.47,-122.43:20:99:47:4 1/0:-10.15,0,-51.55:39:99:34:14 17 58204252 . G A 2018 SC;MQ Source=Platypus;CSQ=A|ENSG00000267248|ENST00000590744|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2319I12.4|lincRNA|||||||;PH=-1.914;PS=0.172;SD=0.99738 GT:GL:GOF:GQ:NR:NV 1/1:-191,-16.28,0:22:99:57:57 1/0:-87.35,0,-75.65:17:99:54:28 17 58224935 . G A 1486 PASS Source=Platypus;CSQ=A|ENSG00000167434|ENST00000585705|Transcript|upstream_gene_variant||||2368|CA4|retained_intron|||||||,A|ENSG00000167434|ENST00000586876|Transcript|upstream_gene_variant||||2368|CA4|nonsense_mediated_decay|||||||,A|ENSG00000167434|ENST00000591725|Transcript|upstream_gene_variant||||2368|CA4|protein_coding|||||||,A|ENSG00000167434|ENST00000300900|Transcript|upstream_gene_variant||||2362|CA4|protein_coding|YES||||||;GR=4.02;PH=2.53;PS=0.999 GT:GL:GOF:GQ:NR:NV 1/1:-257,-17.16,0:3:99:58:51 1/1:-241,-15.95,0:1:99:54:49 17 63045916 . C T 2564 PASS Source=Platypus;CSQ=T|ENSG00000266598|ENST00000581796|Transcript|upstream_gene_variant||||2111|RP11-583F2.5|antisense|YES||||||,T|ENSG00000120063|ENST00000541118|Transcript|intron_variant|||||GNA13|protein_coding|||||||,T|ENSG00000120063|ENST00000439174|Transcript|intron_variant|||||GNA13|protein_coding|YES||||||;GR=-2.03;PH=-0.396;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-6.9,-0.84,0:6:9:25:7 1/1:-15.9,-3.46,0:4:35:35:14 17 63507332 . C T 44 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.451;PS=0.287;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-11.14,-179.7:17:99:46:0 0/1:-97.16,0,-70.76:17:99:37:15 17 65189327 . GG - 39 PASS Source=Platypus;CSQ=-|ENSG00000198265|ENST00000580168|Transcript|intron_variant&feature_truncation|||||HELZ|protein_coding|||||||,-|ENSG00000198265|ENST00000417253|Transcript|intron_variant&feature_truncation|||||HELZ|non_stop_decay|||||||,-|ENSG00000198265|ENST00000578783|Transcript|upstream_gene_variant||||4810|HELZ|protein_coding|||||||,-|ENSG00000198265|ENST00000582864|Transcript|upstream_gene_variant||||3597|HELZ|retained_intron|||||||,-|ENSG00000198265|ENST00000579953|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||HELZ|nonsense_mediated_decay|||||||,-|ENSG00000198265|ENST00000358691|Transcript|intron_variant&feature_truncation|||||HELZ|protein_coding|YES||||||,-|ENSG00000198265|ENST00000578938|Transcript|upstream_gene_variant||||4850|HELZ|processed_transcript|||||||,-|ENSG00000198265|ENST00000580662|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||HELZ|processed_transcript|||||||;GR=0.225;PH=0.3;PS=0.023;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-79.98,0,-81.38:1:99:58:28 1/1:-240.8,-19.85,0:1:99:66:66 17 65664860 . C T 2337 PASS Source=Platypus;CSQ=T|ENSG00000154217|ENST00000580974|Transcript|intron_variant|||||PITPNC1|protein_coding|||||||,T|ENSG00000154217|ENST00000335257|Transcript|intron_variant|||||PITPNC1|protein_coding|||||||,T|ENSG00000154217|ENST00000299954|Transcript|intron_variant|||||PITPNC1|protein_coding|||||||,T|ENSG00000154217|ENST00000578527|Transcript|intron_variant&non_coding_transcript_variant|||||PITPNC1|retained_intron|||||||,T|ENSG00000154217|ENST00000581322|Transcript|intron_variant|||||PITPNC1|protein_coding|YES||||||;GR=0.118;PH=0.191;PS=0.086;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.03,-178.6:4:99:54:0 1/1:-131.1,-10.49,0:0:99:39:39 17 65932055 . G A 1898 PASS Source=Platypus;CSQ=A|ENSG00000171634|ENST00000306378|Transcript|intron_variant|||||BPTF|protein_coding|YES||||||,A|ENSG00000171634|ENST00000577770|Transcript|upstream_gene_variant||||670|BPTF|processed_transcript|||||||,A|ENSG00000171634|ENST00000544778|Transcript|intron_variant|||||BPTF|protein_coding|||||||,A|ENSG00000171634|ENST00000424123|Transcript|intron_variant|||||BPTF|protein_coding|||||||,A|ENSG00000171634|ENST00000584931|Transcript|upstream_gene_variant||||4589|BPTF|retained_intron|||||||,A|ENSG00000171634|ENST00000321892|Transcript|intron_variant|||||BPTF|protein_coding|||||||,A|ENSG00000171634|ENST00000335221|Transcript|intron_variant|||||BPTF|protein_coding|||||||,A|ENSG00000171634|ENST00000580465|Transcript|upstream_gene_variant||||4624|BPTF|protein_coding|||||||,A|ENSG00000171634|ENST00000582467|Transcript|intron_variant|||||BPTF|protein_coding|||||||;GR=-1.26;PH=-0.228;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-171.2,-14.13,0:4:99:50:50 1/1:-187.5,-15.65,0:1:99:56:56 17 66676991 . C T 2233 PASS Source=Platypus;CSQ=T|ENSG00000267659|ENST00000587999|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-118B18.1|lincRNA|||||||,T|ENSG00000267659|ENST00000585484|Transcript|downstream_gene_variant||||1244|RP11-118B18.1|lincRNA|YES||||||,T|ENSG00000267659|ENST00000589610|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-118B18.1|lincRNA|||||||,T|ENSG00000267659|ENST00000591754|Transcript|downstream_gene_variant||||3684|RP11-118B18.1|lincRNA|||||||;GR=0.349;PH=0.433;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-16.56,-208.3:1:99:58:0 1/1:-238,-19.04,0:1:99:67:66 17 67071315 . A G 2322 PASS Source=Platypus;CSQ=G|ENSG00000154262|ENST00000284425|Transcript|downstream_gene_variant||||3528|ABCA6|protein_coding|YES||||||,G|ENSG00000154262|ENST00000446604|Transcript|downstream_gene_variant||||3743|ABCA6|processed_transcript|||||||;GR=0.131;PH=0.148;PS=0.169;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-67.39,0,-68.29:10:99:49:25 0/0:0,-6.92,-84.2:17:69:24:0 17 68581306 . TT - 475 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.235;PH=0.263;PS=0.031;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-13.76,-157.2:6:99:50:0 1/0:-58.09,0,-34.69:6:99:33:18 17 68879818 . G A 915 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.149;PH=0.192;PS=0.036;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-213.1,-16.06,0:2:99:63:62 1/0:-92.85,0,-62.55:1:99:50:29 17 70683502 . CC - 734 PASS Source=Platypus;CSQ=-|ENSG00000133195|ENST00000582769|Transcript|intron_variant&feature_truncation|||||SLC39A11|protein_coding|||||||,-|ENSG00000133195|ENST00000542342|Transcript|intron_variant&feature_truncation|||||SLC39A11|protein_coding|YES||||||,-|ENSG00000133195|ENST00000579988|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||SLC39A11|processed_transcript|||||||,-|ENSG00000133195|ENST00000255559|Transcript|intron_variant&feature_truncation|||||SLC39A11|protein_coding|||||||;GR=0.158;PH=0.202;PS=0.105;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-207.4,-16.82,0:2:99:57:57 1/0:-80.24,0,-101.04:2:99:62:28 17 70918648 . A G 291 PASS Source=Platypus;CSQ=G|ENSG00000133195|ENST00000579732|Transcript|intron_variant|||||SLC39A11|protein_coding|||||||,G|ENSG00000133195|ENST00000580557|Transcript|intron_variant|||||SLC39A11|protein_coding|||||||,G|ENSG00000133195|ENST00000584129|Transcript|intron_variant&NMD_transcript_variant|||||SLC39A11|nonsense_mediated_decay|||||||,G|ENSG00000133195|ENST00000542342|Transcript|intron_variant|||||SLC39A11|protein_coding|YES||||||,G|ENSG00000133195|ENST00000582769|Transcript|intron_variant|||||SLC39A11|protein_coding|||||||,G|ENSG00000133195|ENST00000579491|Transcript|intron_variant&non_coding_transcript_variant|||||SLC39A11|processed_transcript|||||||,G|ENSG00000133195|ENST00000255559|Transcript|intron_variant|||||SLC39A11|protein_coding|||||||,G|ENSG00000133195|ENST00000583146|Transcript|intron_variant|||||SLC39A11|protein_coding|||||||;GR=1.98;PH=1.167;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-74.66,0,-44.26:2:99:38:23 1/1:-150.1,-12.04,0:0:99:42:42 17 76213374 . AG - 2293 PASS Source=Platypus;CSQ=-|ENSG00000089685|ENST00000592115|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||BIRC5|retained_intron|||||||,-|ENSG00000089685|ENST00000301633|Transcript|intron_variant&feature_truncation|||||BIRC5|protein_coding|YES||||||,-|ENSG00000089685|ENST00000586192|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||BIRC5|nonsense_mediated_decay|||||||,-|ENSG00000089685|ENST00000590925|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||BIRC5|nonsense_mediated_decay|||||||,-|ENSG00000089685|ENST00000589892|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||BIRC5|processed_transcript|||||||,-|ENSG00000089685|ENST00000591800|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||BIRC5|nonsense_mediated_decay|||||||,-|ENSG00000268310|ENST00000600484|Transcript|intron_variant&feature_truncation|||||AC087645.1|protein_coding|YES||||||,-|ENSG00000089685|ENST00000350051|Transcript|intron_variant&feature_truncation|||||BIRC5|protein_coding|||||||,-|ENSG00000089685|ENST00000592734|Transcript|intron_variant&feature_truncation|||||BIRC5|protein_coding|||||||,-|ENSG00000089685|ENST00000587746|Transcript|intron_variant&feature_truncation|||||BIRC5|protein_coding|||||||,-|ENSG00000089685|ENST00000374948|Transcript|intron_variant&feature_truncation|||||BIRC5|protein_coding|||||||,-|ENSG00000089685|ENST00000590449|Transcript|downstream_gene_variant||||2194|BIRC5|protein_coding|||||||;GR=0.354;PH=0.338;PS=0.01;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-166.1,-13.85,0:32:99:49:49 1/1:-175.8,-14.72,0:27:99:51:50 18 409982 rs529926380 C T 771 PASS Source=Platypus;CSQ=T|ENSG00000158270|ENST00000582147|Transcript|intron_variant&non_coding_transcript_variant|||||COLEC12|retained_intron|||||||,T|ENSG00000158270|ENST00000400256|Transcript|intron_variant|||||COLEC12|protein_coding|YES||||||;GR=1.59;PH=0.432;PS=0.094;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-81.7,0,-56.2:8:99:51:29 0/0:0,-14.15,-167.5:9:99:52:0 18 1508245 . A G 2911 PASS Source=Platypus;CSQ=G|ENSG00000266602|ENST00000583163|Transcript|upstream_gene_variant||||939|RP11-476K15.1|lincRNA|YES||||||;GR=0.149;PH=0.166;PS=0.051;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-43.3,-2.96,0:47:30:13:12 0/1:-19.1,0,-45.2:20:99:17:5 18 4373697 . T C 994 PASS Source=Platypus;CSQ=C|ENSG00000170579|ENST00000581527|Transcript|intron_variant|||||DLGAP1|protein_coding|||||||,C|ENSG00000170579|ENST00000315677|Transcript|intron_variant|||||DLGAP1|protein_coding|YES||||||;GR=1.07;PH=0.293;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.65,-300:5:99:51:0 1/0:-300,0,-300:1:99:48:20 18 8627710 . CC - 452 PASS Source=Platypus;CSQ=-|ENSG00000206418|ENST00000329286|Transcript|intron_variant&feature_truncation|||||RAB12|protein_coding|YES||||||,-||ENSR00001513028|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.162;PH=0.005;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-81.25,0,-71.15:8:99:54:29 0/1:-75.85,0,-75.75:1:99:51:24 18 9133566 . T C 2677 PASS Source=Platypus;CSQ=C|ENSG00000101745|ENST00000540578|Transcript|upstream_gene_variant||||3237|ANKRD12|processed_transcript|||||||,C|ENSG00000101745|ENST00000585234|Transcript|upstream_gene_variant||||2660|ANKRD12|protein_coding|||||||,C|ENSG00000265257|ENST00000579126|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-21J18.1|processed_transcript|YES||||||,C|ENSG00000178127|ENST00000474740|Transcript|intron_variant&non_coding_transcript_variant|||||NDUFV2|processed_transcript|||||||,C|ENSG00000266053|ENST00000583081|Transcript|upstream_gene_variant||||146|RP11-143J12.2|antisense|||||||,C|ENSG00000178127|ENST00000465096|Transcript|intron_variant&non_coding_transcript_variant|||||NDUFV2|processed_transcript|||||||,C|ENSG00000101745|ENST00000577992|Transcript|upstream_gene_variant||||3228|ANKRD12|protein_coding|||||||,C|ENSG00000265257|ENST00000578850|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-21J18.1|processed_transcript|||||||,C|ENSG00000101745|ENST00000383440|Transcript|upstream_gene_variant||||3192|ANKRD12|protein_coding|||||||,C|ENSG00000101745|ENST00000581635|Transcript|upstream_gene_variant||||3271|ANKRD12|nonsense_mediated_decay|||||||,C|ENSG00000266053|ENST00000582375|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-143J12.2|antisense|||||||,C|ENSG00000101745|ENST00000262126|Transcript|upstream_gene_variant||||3209|ANKRD12|protein_coding|YES||||||,C|ENSG00000178127|ENST00000318388|Transcript|intron_variant|||||NDUFV2|protein_coding|YES||||||,C|ENSG00000266053|ENST00000608008|Transcript|downstream_gene_variant||||2145|RP11-143J12.2|antisense|YES||||||,C|ENSG00000178127|ENST00000400033|Transcript|intron_variant|||||NDUFV2|protein_coding|||||||,C|ENSG00000101745|ENST00000400020|Transcript|upstream_gene_variant||||3995|ANKRD12|protein_coding|||||||;GR=0.496;PH=0.353;PS=0.004 GT:GL:GOF:GQ:NR:NV 0/1:-11.99,0,-7.99:27:80:26:4 0/1:-9.92,0,-8.42:30:84:33:12 18 13763343 . C T 2075 PASS Source=Platypus;CSQ=T|ENSG00000101654|ENST00000588457|Transcript|downstream_gene_variant||||1000|RNMT|nonsense_mediated_decay|||||||,T|ENSG00000101654|ENST00000383314|Transcript|3_prime_UTR_variant|5036||||RNMT|protein_coding|YES||||||,T|ENSG00000101654|ENST00000593007|Transcript|downstream_gene_variant||||717|RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000262173|Transcript|3_prime_UTR_variant|4840||||RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000589866|Transcript|downstream_gene_variant||||3277|RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000592764|Transcript|3_prime_UTR_variant|2896||||RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000535051|Transcript|downstream_gene_variant||||1269|RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000543302|Transcript|downstream_gene_variant||||3059|RNMT|protein_coding|||||||,T|ENSG00000101654|ENST00000591922|Transcript|intron_variant&non_coding_transcript_variant|||||RNMT|processed_transcript|||||||;GR=-1.43;PH=-0.42;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-267.2,-21.67,0:15:99:73:73 0/0:0,-20.45,-253.4:2:99:69:0 18 19067700 . GCCT - 39 PASS Source=Platypus;CSQ=-|ENSG00000141449|ENST00000269218|Transcript|intron_variant&feature_truncation|||||GREB1L|protein_coding|||||||,-|ENSG00000141449|ENST00000578383|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||GREB1L|retained_intron|||||||,-|ENSG00000141449|ENST00000424526|Transcript|intron_variant&feature_truncation|||||GREB1L|protein_coding|||||||,-|ENSG00000141449|ENST00000578955|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||GREB1L|retained_intron|||||||,-|ENSG00000141449|ENST00000400483|Transcript|intron_variant&feature_truncation|||||GREB1L|protein_coding|||||||,-|ENSG00000141449|ENST00000580732|Transcript|intron_variant&feature_truncation|||||GREB1L|protein_coding|YES||||||;GR=0.131;PH=0.173;PS=0.063;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-138.7,-11.74,0:3:99:43:43 1/1:-138.7,-11.74,0:2:99:41:41 18 20080977 . A G 2870 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.501;PH=0.431;PS=0.013;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-80.2,-7.83,0:9:78:48:25 1/1:-79.3,-6.98,0:6:70:39:26 18 30062614 . A G 95 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.27;PH=0.27;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-70.57,0,-66.67:2:99:51:25 0/0:0,-17.46,-215.9:3:99:58:0 18 32294551 . G A 523 PASS Source=Platypus;CSQ=A|ENSG00000134769|ENST00000588684|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000588125|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000348997|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000598334|Transcript|intron_variant|||||DTNA|protein_coding|YES||||||,A|ENSG00000134769|ENST00000315456|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000588949|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000598774|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000591816|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000597599|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000585446|Transcript|intron_variant&non_coding_transcript_variant|||||DTNA|processed_transcript|||||||,A|ENSG00000134769|ENST00000590598|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000399121|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000269190|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000590412|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000596745|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000598142|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000554864|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000595022|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000283365|Transcript|intron_variant|||||DTNA|protein_coding|||||||,A|ENSG00000134769|ENST00000399097|Transcript|intron_variant|||||DTNA|protein_coding|||||||;PH=0.064;PS=0.179;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-4.07,0,-1.57:6:16:22:4 0/1:-1.31,0,-5.81:3:13:27:2 18 33843993 . G A 2790 PASS Source=Platypus;CSQ=A|ENSG00000075643|ENST00000588132|Transcript|intron_variant&non_coding_transcript_variant|||||MOCOS|processed_transcript|||||||,A|ENSG00000075643|ENST00000261326|Transcript|intron_variant|||||MOCOS|protein_coding|YES||||||;GR=0.235;PH=0.308;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-170.5,-14.65,0:8:99:52:52 1/1:-251.4,-19.87,0:0:99:69:69 18 37569676 . C T 2678 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-1.07;PH=-0.723;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-82.14,0,-88.44:2:99:58:28 0/0:0,-12.89,-153.7:3:99:46:1 18 38566162 . C T 2054 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.518;PH=0.175;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-104.2,0,-80.7:11:99:70:37 1/0:-60.78,0,-89.98:3:99:53:22 18 39868241 . T C 111 PASS Source=Platypus;CSQ=C|ENSG00000267586|ENST00000586990|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000593051|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000585627|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000589068|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000593234|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|YES||||||,C|ENSG00000267586|ENST00000591199|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000591381|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000593316|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||,C|ENSG00000267586|ENST00000585639|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00907|lincRNA|||||||;GR=0.948;PH=0.228;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-89.88,0,-94.38:1:99:63:31 0/0:0,-18.34,-218.4:4:99:62:0 18 42235677 . CT - 1914 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.84;PH=0.28;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/0:-96.85,0,-134.75:2:99:57:16 0/0:0,-12.34,-250.8:8:99:56:12 18 43808864 . TA - 2732 PASS Source=Platypus;CSQ=-|ENSG00000152242|ENST00000321319|Transcript|intron_variant&feature_truncation|||||C18orf25|protein_coding|||||||,-|ENSG00000152242|ENST00000282059|Transcript|intron_variant&feature_truncation|||||C18orf25|protein_coding|YES||||||,-|ENSG00000152242|ENST00000588730|Transcript|intron_variant&feature_truncation|||||C18orf25|protein_coding|||||||;GR=2.76;PH=0.845;PS=0.004 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.16,-203.2:1:99:59:1 1/0:-56.67,0,-47.07:2:99:35:19 18 45078720 . C T 1332 PASS Source=Platypus;CSQ=T|ENSG00000267761|ENST00000586905|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2130O13.1|lincRNA|||||||,T|ENSG00000261307|ENST00000565127|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-157P23.2|lincRNA|YES||||||,T|ENSG00000267761|ENST00000598649|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2130O13.1|lincRNA|||||||;GR=2.43;PH=0.971;PS=0.01 GT:GL:GOF:GQ:NR:NV 1/1:-191.5,-15.92,0:3:99:57:57 0/0:0,-16.26,-204.5:1:99:56:0 18 46001292 . T C 832 PASS Source=Platypus;CSQ=C|ENSG00000266984|ENST00000588366|Transcript|upstream_gene_variant||||3640|RP11-23B5.1|processed_pseudogene|YES||||||,C|ENSG00000200872|ENST00000364002|Transcript|downstream_gene_variant||||566|RNA5SP456|rRNA|YES||||||;GR=-0.346;PH=-0.078;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-57.86,0,-70.76:36:99:41:19 1/1:-183.2,-15.05,0:93:99:53:53 18 48503168 . T C 613 PASS Source=Platypus;CSQ=C|ENSG00000141642|ENST00000591429|Transcript|intron_variant|||||ELAC1|protein_coding|||||||,C|ENSG00000267699|ENST00000588256|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-729L2.2|processed_transcript|||||||,C|ENSG00000267699|ENST00000590722|Transcript|intron_variant&NMD_transcript_variant|||||RP11-729L2.2|nonsense_mediated_decay|YES||||||,C|ENSG00000141642|ENST00000269466|Transcript|intron_variant|||||ELAC1|protein_coding|YES||||||,C|ENSG00000141646|ENST00000452201|Transcript|intron_variant|||||SMAD4|protein_coding|||||||,C|ENSG00000141642|ENST00000588577|Transcript|intron_variant|||||ELAC1|protein_coding|||||||;GR=0.122;PH=0.166;PS=0.043;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-60.1,0,-68.8:5:99:49:24 1/1:-149.5,-12.34,0:7:99:44:44 18 50724811 . C T 1307 PASS Source=Platypus;CSQ=T|ENSG00000187323|ENST00000581580|Transcript|intron_variant|||||DCC|protein_coding|||||||,T|ENSG00000187323|ENST00000304775|Transcript|intron_variant&NMD_transcript_variant|||||DCC|nonsense_mediated_decay|||||||,T|ENSG00000187323|ENST00000442544|Transcript|intron_variant|||||DCC|protein_coding|YES||||||,T|ENSG00000187323|ENST00000412726|Transcript|intron_variant|||||DCC|protein_coding|||||||;GR=-1.03;PH=-0.31;PS=0;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 1/1:-180.1,-15.05,0:2:99:54:52 1/1:-187.8,-15.05,0:0:99:52:52 18 51317700 . A G 401 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-0.01;PH=-0.061;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.76,-209.9:6:99:60:0 1/0:-67.36,0,-53.36:3:99:42:24 18 55411356 . GG - 494 PASS Source=Platypus;CSQ=-|ENSG00000081923|ENST00000585322|Transcript|upstream_gene_variant||||3159|ATP8B1|protein_coding|||||||,-|ENSG00000081923|ENST00000591728|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ATP8B1|nonsense_mediated_decay|||||||,-|ENSG00000081923|ENST00000536015|Transcript|intron_variant&feature_truncation|||||ATP8B1|protein_coding|YES||||||;GR=-0.335;PH=-1.05;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-75.57,0,-92.97:1:99:58:26 1/0:-55.7,0,-55.6:0:99:40:20 18 55433348 . T C 496 PASS Source=Platypus;CSQ=C|ENSG00000081923|ENST00000591728|Transcript|intron_variant&NMD_transcript_variant|||||ATP8B1|nonsense_mediated_decay|||||||,C|ENSG00000081923|ENST00000536015|Transcript|intron_variant|||||ATP8B1|protein_coding|YES||||||;GR=0.167;PH=0.237;PS=0.012;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-79.66,0,-53.06:2:99:45:25 1/1:-186.7,-15.05,0:0:99:50:50 18 60210549 . C T 2566 PASS Source=Platypus;CSQ=T|ENSG00000141664|ENST00000585873|Transcript|intron_variant&NMD_transcript_variant|||||ZCCHC2|nonsense_mediated_decay|||||||,T|ENSG00000141664|ENST00000586834|Transcript|intron_variant|||||ZCCHC2|protein_coding|||||||,T|ENSG00000141664|ENST00000269499|Transcript|intron_variant|||||ZCCHC2|protein_coding|YES||||||,T|ENSG00000141664|ENST00000591632|Transcript|intron_variant&non_coding_transcript_variant|||||ZCCHC2|processed_transcript|||||||;GR=-7.97;PH=-1.655;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-76.82,0,-93.02:8:99:56:26 1/1:-232.7,-18.94,0:27:99:65:65 18 60633197 . AACT - 2430 PASS Source=Platypus;CSQ=-|ENSG00000081913|ENST00000400316|Transcript|intron_variant&feature_truncation|||||PHLPP1|protein_coding|||||||,-|ENSG00000081913|ENST00000262719|Transcript|intron_variant&feature_truncation|||||PHLPP1|protein_coding|YES||||||;GR=0.949;PH=0.094;PS=0.015 GT:GL:GOF:GQ:NR:NV 0/1:-42.43,0,-85.73:4:99:70:19 1/1:-85.1,-12.03,0:5:99:41:19 18 61553218 . TAAC - 804 PASS Source=Platypus;CSQ=-|ENSG00000197632|ENST00000413956|Transcript|upstream_gene_variant||||1772|SERPINB2|protein_coding|||||||,-|ENSG00000197632|ENST00000457692|Transcript|upstream_gene_variant||||1718|SERPINB2|protein_coding|YES||||||,-|ENSG00000197632|ENST00000443281|Transcript|upstream_gene_variant||||4570|SERPINB2|protein_coding|||||||,-|ENSG00000197632|ENST00000299502|Transcript|upstream_gene_variant||||1713|SERPINB2|protein_coding|||||||,-|ENSG00000197632|ENST00000404622|Transcript|intron_variant&feature_truncation|||||SERPINB2|protein_coding|||||||,-||ENSR00000527529|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.64;PH=0.417;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-14.75,-187.6:1:99:49:0 1/1:-166.1,-13.25,0:2:99:44:44 18 65346933 . A G 47 PASS Source=Platypus;CSQ=G|ENSG00000263594|ENST00000578039|Transcript|upstream_gene_variant||||3618|RP11-28O3.2|lincRNA|YES||||||,G|ENSG00000265533|ENST00000583687|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-638L3.1|lincRNA|YES||||||;GR=0.109;PH=0.156;PS=0.015;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.96,-225.7:11:99:66:0 1/0:-81.66,0,-79.56:6:99:61:29 18 66570911 . TA - 2222 PASS Source=Platypus;CSQ=-|ENSG00000264472|ENST00000584226|Transcript|upstream_gene_variant||||1419|RP11-861L17.3|processed_transcript|||||||,-|ENSG00000150636|ENST00000584156|Transcript|intron_variant&feature_truncation|||||CCDC102B|protein_coding|||||||,-|ENSG00000150636|ENST00000319445|Transcript|intron_variant&feature_truncation|||||CCDC102B|protein_coding|||||||,-|ENSG00000150636|ENST00000360242|Transcript|intron_variant&feature_truncation|||||CCDC102B|protein_coding|YES||||||,-|ENSG00000264472|ENST00000579678|Transcript|upstream_gene_variant||||1419|RP11-861L17.3|protein_coding|YES||||||;GR=0.975;PH=0.355;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.92,-151.4:27:99:49:0 1/0:-67.95,0,-69.05:27:99:48:23 18 67406043 . CA - 1106 PASS Source=Platypus;CSQ=-|ENSG00000206052|ENST00000584435|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||DOK6|processed_transcript|||||||,-|ENSG00000206052|ENST00000577609|Transcript|upstream_gene_variant||||177|DOK6|processed_transcript|||||||,-|ENSG00000206052|ENST00000582992|Transcript|intron_variant&feature_truncation|||||DOK6|protein_coding|||||||,-|ENSG00000206052|ENST00000382713|Transcript|intron_variant&feature_truncation|||||DOK6|protein_coding|YES||||||;GR=-3.01;PH=-0.659;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-47.36,0,-72.86:2:99:40:16 0/0:0,-6.32,-78.3:0:63:22:0 18 67962461 . A G 2548 PASS Source=Platypus;CSQ=G|ENSG00000170677|ENST00000578377|Transcript|upstream_gene_variant||||1374|SOCS6|protein_coding|||||||,G|ENSG00000170677|ENST00000397942|Transcript|intron_variant|||||SOCS6|protein_coding|YES||||||;GR=-2.03;PH=-0.42;PS=0 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:7:99:100,94:46,46 1/2:-1,-1,-1:19:99:93,92:44,44 18 70276626 . C T 1085 PASS Source=Platypus;CSQ=T|ENSG00000141668|ENST00000580889|Transcript|intron_variant&non_coding_transcript_variant|||||CBLN2|processed_transcript|||||||,T|ENSG00000141668|ENST00000581073|Transcript|intron_variant|||||CBLN2|protein_coding|||||||;GR=0.612;PH=0.197;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-162.4,-13.55,0:13:99:45:44 0/1:-68.45,0,-87.75:1:99:51:23 18 70949309 . TAA - 2886 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.149;PH=0.166;PS=0.01;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV ./.:-0.01,0,-2.44:7:3:5:0 0/1:-13.38,0,-3.7:13:37:27:8 18 71023311 . A G 1862 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-0.0288;PH=-0.008;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-216.1,-17.72,0:2:99:61:61 1/0:-101.27,0,-76.97:4:99:60:34 18 71184770 . CT - 2468 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.073;PS=0.085;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-4.62,-74.2:126:46:27:0 0/1:-21.29,0,-68.09:109:99:38:8 18 73348055 . A G 1050 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-0.648;PH=-0.153;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-82.59,0,-49.59:1:99:46:27 0/0:0,-20.13,-242:11:99:69:0 19 816022 . C T 1510 PASS Source=Platypus;CSQ=T|ENSG00000011304|ENST00000349038|Transcript|downstream_gene_variant||||3702|PTBP1|protein_coding|||||||,T|ENSG00000129951|ENST00000520876|Transcript|intron_variant|||||LPPR3|protein_coding|||||||,T|ENSG00000011304|ENST00000394601|Transcript|downstream_gene_variant||||3702|PTBP1|protein_coding|||||||,T|ENSG00000011304|ENST00000356948|Transcript|downstream_gene_variant||||3702|PTBP1|protein_coding|YES||||||,T|ENSG00000129951|ENST00000519502|Transcript|intron_variant|||||LPPR3|protein_coding|||||||,T|ENSG00000011304|ENST00000350092|Transcript|downstream_gene_variant||||3695|PTBP1|protein_coding|||||||,T|ENSG00000129951|ENST00000517665|Transcript|upstream_gene_variant||||1273|LPPR3|protein_coding|||||||,T|ENSG00000011304|ENST00000586944|Transcript|downstream_gene_variant||||4733|PTBP1|retained_intron|||||||,T|ENSG00000129951|ENST00000359894|Transcript|intron_variant|||||LPPR3|protein_coding|YES||||||,T|ENSG00000263414|ENST00000583431|Transcript|downstream_gene_variant||||2369|MIR3187|miRNA|YES||||||,T||ENSR00000640642|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.352;PH=-0.009;PS=0;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/1:-30.41,0,-38.81:6:99:29:13 0/0:0,-7.22,-82.6:3:72:25:0 19 1487482 . GG - 547 PASS Source=Platypus;CSQ=-|ENSG00000115255|ENST00000233596|Transcript|upstream_gene_variant||||3682|REEP6|protein_coding|YES||||||,-|ENSG00000115257|ENST00000590057|Transcript|downstream_gene_variant||||300|PCSK4|processed_transcript|||||||,-|ENSG00000115257|ENST00000588671|Transcript|intron_variant&feature_truncation|||||PCSK4|protein_coding|||||||,-|ENSG00000115257|ENST00000591201|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PCSK4|nonsense_mediated_decay|||||||,-|ENSG00000267715|ENST00000585643|Transcript|downstream_gene_variant||||2209|CTB-25B13.6|antisense|YES||||||,-|ENSG00000115257|ENST00000587784|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PCSK4|processed_transcript|||||||,-|ENSG00000115257|ENST00000586616|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PCSK4|retained_intron|||||||,-|ENSG00000115257|ENST00000588195|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PCSK4|nonsense_mediated_decay|||||||,-|ENSG00000115257|ENST00000300954|Transcript|intron_variant&feature_truncation|||||PCSK4|protein_coding|YES||||||,-|ENSG00000115255|ENST00000591735|Transcript|upstream_gene_variant||||3709|REEP6|retained_intron|||||||,-|ENSG00000115257|ENST00000586074|Transcript|upstream_gene_variant||||4816|PCSK4|retained_intron|||||||,-|ENSG00000115257|ENST00000441747|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PCSK4|retained_intron|||||||,-|ENSG00000115257|ENST00000591303|Transcript|upstream_gene_variant||||3639|PCSK4|nonsense_mediated_decay|||||||,-|ENSG00000115257|ENST00000591687|Transcript|downstream_gene_variant||||479|PCSK4|processed_transcript|||||||,-|ENSG00000115257|ENST00000586002|Transcript|upstream_gene_variant||||3356|PCSK4|retained_intron|||||||;GR=0.1;PH=0.116;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:0:99:49,49:29,29 2/2:-1,-1,-1:1:99:63,63:28,28 19 3107620 . TAGC - 268 PASS Source=Platypus;CSQ=-|ENSG00000088256|ENST00000586763|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||GNA11|processed_transcript|||||||,-|ENSG00000088256|ENST00000078429|Transcript|intron_variant&feature_truncation|||||GNA11|protein_coding|YES||||||;GR=0.898;PH=0.695;PS=0.007 GT:GL:GOF:GQ:NR:NV 1/1:-155.6,-13.46,0:2:99:47:46 1/1:-132.8,-11.53,0:1:99:40:40 19 5159959 . CC - 837 PASS Source=Platypus;CSQ=-|ENSG00000105426|ENST00000588552|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PTPRS|processed_transcript|||||||;PH=0.119;PS=0.011;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-59.75,0,-86.15:1:99:49:21 0/0:0,-15.05,-187.6:0:99:51:0 19 6455950 rs189078682 G A 67 PASS Source=Platypus;CSQ=A|ENSG00000125648|ENST00000597307|Transcript|downstream_gene_variant||||481|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000301454|Transcript|intron_variant|||||SLC25A23|protein_coding|YES||||||,A|ENSG00000125648|ENST00000597039|Transcript|upstream_gene_variant||||3338|SLC25A23|retained_intron|||||||,A|ENSG00000125648|ENST00000334510|Transcript|intron_variant|||||SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000601322|Transcript|upstream_gene_variant||||1563|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000598908|Transcript|upstream_gene_variant||||1269|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000595267|Transcript|downstream_gene_variant||||364|SLC25A23|retained_intron|||||||,A|ENSG00000125648|ENST00000414491|Transcript|upstream_gene_variant||||1269|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000264088|Transcript|intron_variant&NMD_transcript_variant|||||SLC25A23|nonsense_mediated_decay|||||||,A|ENSG00000125648|ENST00000595810|Transcript|upstream_gene_variant||||1930|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000593600|Transcript|upstream_gene_variant||||1534|SLC25A23|protein_coding|||||||,A|ENSG00000125648|ENST00000598704|Transcript|upstream_gene_variant||||3551|SLC25A23|nonsense_mediated_decay|||||||,A|ENSG00000125648|ENST00000600682|Transcript|upstream_gene_variant||||1269|SLC25A23|protein_coding|||||||;GR=-0.317;PH=-1.129;PS=0.005;REPMASK=SINE;1000G=0.000399361;ExAC=3/18532 GT:GL:GOF:GQ:NR:NV 1/1:-299.4,-19.86,0:2:99:74:58 0/0:0,-16.23,-264:1:99:62:0 19 9648156 . GAG - 1648 PASS Source=Platypus;CSQ=-|ENSG00000130818|ENST00000535489|Transcript|upstream_gene_variant||||911|ZNF426|protein_coding|YES||||||,-|ENSG00000130818|ENST00000253115|Transcript|intron_variant&feature_truncation|||||ZNF426|protein_coding|||||||,-|ENSG00000130818|ENST00000589289|Transcript|intron_variant&feature_truncation|||||ZNF426|protein_coding|||||||,-|ENSG00000130818|ENST00000593003|Transcript|intron_variant&feature_truncation|||||ZNF426|protein_coding|||||||;GR=0.158;PH=0.202;PS=0.036;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-46.17,0,-89.37:4:99:50:18 0/1:-81.45,0,-69.75:1:99:53:29 19 11413443 . G A 100 PASS Source=Platypus;CSQ=A|ENSG00000130167|ENST00000337994|Transcript|intron_variant&NMD_transcript_variant|||||TSPAN16|nonsense_mediated_decay|||||||,A|ENSG00000267174|ENST00000585801|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-510F12.4|3prime_overlapping_ncrna|||||||,A|ENSG00000130167|ENST00000592955|Transcript|intron_variant|||||TSPAN16|protein_coding|||||||,A|ENSG00000267174|ENST00000586356|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-510F12.4|3prime_overlapping_ncrna|YES||||||,A|ENSG00000130167|ENST00000316737|Transcript|intron_variant|||||TSPAN16|protein_coding|YES||||||,A|ENSG00000130167|ENST00000589928|Transcript|upstream_gene_variant||||3957|TSPAN16|nonsense_mediated_decay|||||||,A|ENSG00000130167|ENST00000590327|Transcript|intron_variant|||||TSPAN16|protein_coding|||||||;GR=0.0465;PH=0.132;PS=0.435;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-185.3,-15.35,0:7:99:53:53 1/1:-191.4,-15.05,0:1:99:52:52 19 11780790 . T C 1714 PASS Source=Platypus;CSQ=C|ENSG00000197332|ENST00000344893|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF833P|lincRNA|YES||||||,C|ENSG00000214223|ENST00000444945|Transcript|upstream_gene_variant||||2945|HNRNPA1P10|processed_pseudogene|YES||||||,C|ENSG00000214223|ENST00000406078|Transcript|upstream_gene_variant||||2945|HNRNPA1P10|pseudogene|||||||;GR=0.1;PH=0.147;PS=0.121;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-167.4,-13.55,0:57:99:46:46 1/1:-177.4,-14.45,0:51:99:51:51 19 12317948 . A G 964 PASS Source=Platypus;CSQ=G|ENSG00000234773|ENST00000451691|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2666L21.1|lincRNA|||||||,G|ENSG00000234773|ENST00000426044|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2666L21.1|lincRNA|YES||||||,G|ENSG00000234773|ENST00000440004|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2666L21.1|lincRNA|||||||,G|ENSG00000234773|ENST00000415793|Transcript|intron_variant&non_coding_transcript_variant|||||CTD-2666L21.1|lincRNA|||||||;GR=-1.83;PH=-0.56;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-14.46,-174.3:8:99:58:1 1/0:-51.75,0,-89.15:1:99:48:21 19 12458997 rs577805896 A G 1577 PASS Source=Platypus;CSQ=G|ENSG00000198342|ENST00000424168|Transcript|downstream_gene_variant||||2733|ZNF442|protein_coding|||||||,G|ENSG00000261280|ENST00000563695|Transcript|upstream_gene_variant||||245|CTD-3105H18.13|lincRNA|YES||||||,G|ENSG00000198342|ENST00000462995|Transcript|downstream_gene_variant||||3608|ZNF442|retained_intron|||||||,G|ENSG00000198342|ENST00000438182|Transcript|downstream_gene_variant||||1400|ZNF442|protein_coding|||||||,G|ENSG00000198342|ENST00000242804|Transcript|downstream_gene_variant||||1188|ZNF442|protein_coding|YES||||||;GR=0.158;PH=0.175;PS=0.036;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 1/1:-188.7,-15.35,0:10:99:53:53 1/1:-202.4,-16.26,0:9:99:58:58 19 13783015 rs141045962 G A 2846 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.783;PH=-0.682;PS=0.003;REPMASK=SINE;UK10K=1/7562;1000G=0.00978435 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.64,-151:4:99:48:0 1/0:-77.6,0,-57.8:2:99:49:28 19 15207152 . TG - 620 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.077;PS=0.441;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-25.01,0,-28.51:12:99:43:24 1/0:-40.76,0,-14.64:18:99:45:31 19 15548264 . A G 2274 PASS Source=Platypus;CSQ=G|ENSG00000011451|ENST00000263381|Transcript|intron_variant|||||WIZ|protein_coding|YES||||||,G|ENSG00000011451|ENST00000595214|Transcript|intron_variant&non_coding_transcript_variant|||||WIZ|retained_intron|||||||,G|ENSG00000011451|ENST00000599686|Transcript|upstream_gene_variant||||4896|WIZ|protein_coding|||||||,G|ENSG00000011451|ENST00000596159|Transcript|intron_variant|||||WIZ|protein_coding|||||||,G|ENSG00000011451|ENST00000389282|Transcript|intron_variant|||||WIZ|protein_coding|||||||,G|ENSG00000011451|ENST00000599910|Transcript|upstream_gene_variant||||4163|WIZ|protein_coding|||||||;GR=-1.79;PH=-0.716;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-219.2,-18,0:1:99:63:62 1/1:-225.4,-18.34,0:3:99:61:61 19 19436172 . AA - 2671 PASS Source=Platypus;CSQ=-|ENSG00000105705|ENST00000587716|Transcript|upstream_gene_variant||||4865|SUGP1|processed_transcript|||||||,-|ENSG00000105705|ENST00000606725|Transcript|upstream_gene_variant||||4866|SUGP1|processed_transcript|||||||,-|ENSG00000129933|ENST00000392313|Transcript|intron_variant&feature_truncation|||||MAU2|protein_coding|YES||||||,-|ENSG00000105705|ENST00000587119|Transcript|upstream_gene_variant||||4854|SUGP1|nonsense_mediated_decay|||||||,-|ENSG00000129933|ENST00000262815|Transcript|intron_variant&feature_truncation|||||MAU2|protein_coding|||||||,-|ENSG00000105705|ENST00000247001|Transcript|upstream_gene_variant||||4519|SUGP1|protein_coding|YES||||||,-|ENSG00000105705|ENST00000585444|Transcript|upstream_gene_variant||||4854|SUGP1|nonsense_mediated_decay|||||||,-|ENSG00000105705|ENST00000590439|Transcript|upstream_gene_variant||||4854|SUGP1|protein_coding|||||||,-|ENSG00000105705|ENST00000334782|Transcript|upstream_gene_variant||||4854|SUGP1|protein_coding|||||||,-|ENSG00000105705|ENST00000585763|Transcript|upstream_gene_variant||||4854|SUGP1|processed_transcript|||||||,-|ENSG00000105705|ENST00000591350|Transcript|upstream_gene_variant||||4854|SUGP1|nonsense_mediated_decay|||||||,-|ENSG00000129933|ENST00000609122|Transcript|intron_variant&feature_truncation|||||MAU2|protein_coding|||||||,-|ENSG00000129933|ENST00000586189|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MAU2|processed_transcript|||||||,-|ENSG00000105705|ENST00000535070|Transcript|upstream_gene_variant||||4854|SUGP1|nonsense_mediated_decay|||||||,-|ENSG00000105705|ENST00000588580|Transcript|upstream_gene_variant||||4893|SUGP1|retained_intron|||||||,-|ENSG00000105705|ENST00000588731|Transcript|upstream_gene_variant||||4854|SUGP1|nonsense_mediated_decay|||||||;GR=0.195;PH=0.257;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-78.35,0,-73.45:3:99:55:30 0/1:-72.38,0,-53.98:3:99:52:25 19 20131479 . CCCT - 249 PASS Source=Platypus;CSQ=-|ENSG00000197124|ENST00000358523|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000596019|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000595534|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ZNF682|nonsense_mediated_decay|||||||,-|ENSG00000197124|ENST00000397165|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|YES||||||,-|ENSG00000197124|ENST00000602079|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000593468|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000597972|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000397162|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000595736|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||,-|ENSG00000197124|ENST00000601100|Transcript|intron_variant&feature_truncation|||||ZNF682|protein_coding|||||||;PH=0.159;PS=0.006;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 2/3:-1,-1,-1:5:99:34,34,34:17,17,17 1/2:-1,-1,-1:7:99:16,16,16:9,9,9 19 20242577 . GT - 2488 PASS Source=Platypus;CSQ=-|ENSG00000267220|ENST00000592921|Transcript|downstream_gene_variant||||125|CTC-260E6.9|transcribed_unprocessed_pseudogene|YES||||||,-|ENSG00000267383|ENST00000590606|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTC-260E6.6|antisense|||||||,-|ENSG00000267383|ENST00000586657|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTC-260E6.6|antisense|||||||,-|ENSG00000213988|ENST00000474284|Transcript|downstream_gene_variant||||4692|ZNF90|processed_transcript|||||||,-|ENSG00000267383|ENST00000593655|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTC-260E6.6|antisense|||||||,-|ENSG00000213988|ENST00000469078|Transcript|downstream_gene_variant||||4750|ZNF90|nonsense_mediated_decay|||||||;PH=-1.843;PS=0.01;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-151.8,-12.64,0:3:99:48:47 1/1:-116,-9.33,0:3:93:34:34 19 21394136 . A G 1134 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-0.504;PH=0.165;PS=0.081 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.4,-212.5:2:99:61:0 0/1:-135.33,0,-79.33:1:99:70:42 19 24095274 . TTA - 2903 PASS Source=Platypus;CSQ=-|ENSG00000213967|ENST00000322487|Transcript|upstream_gene_variant||||2436|ZNF726|protein_coding|||||||,-|ENSG00000213967|ENST00000531821|Transcript|upstream_gene_variant||||2408|ZNF726|protein_coding|||||||,-|ENSG00000213967|ENST00000334589|Transcript|upstream_gene_variant||||2403|ZNF726|protein_coding|||||||,-|ENSG00000213967|ENST00000525354|Transcript|upstream_gene_variant||||2402|ZNF726|protein_coding|||||||,-|ENSG00000213967|ENST00000575986|Transcript|upstream_gene_variant||||2445|ZNF726|protein_coding|||||||,-|ENSG00000213967|ENST00000594466|Transcript|upstream_gene_variant||||2416|ZNF726|protein_coding|YES||||||;PH=0.103;PS=0.059;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-81.87,0,-113.57:11:99:69:29 0/0:0,-15.81,-177:2:99:56:0 19 24359356 . C T 742 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.064;PS=0.078;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-55.46,0,-67.06:6:99:44:20 1/0:-68.46,0,-56.86:2:99:42:23 19 27899184 . A G 601 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;REPMASK=Satellite GT:GL:GOF:GQ:NR:NV 0/1:-58.79,0,-62.89:7:99:48:25 0/1:-52.06,0,-64.46:2:99:44:19 19 28265213 . ATAT - 2764 PASS Source=Platypus;CSQ=-|ENSG00000261824|ENST00000586248|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00662|lincRNA|||||||,-|ENSG00000261824|ENST00000588150|Transcript|upstream_gene_variant||||2473|LINC00662|lincRNA|||||||,-|ENSG00000261824|ENST00000590677|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00662|lincRNA|||||||,-|ENSG00000261824|ENST00000586954|Transcript|downstream_gene_variant||||1449|LINC00662|lincRNA|||||||,-|ENSG00000261824|ENST00000591338|Transcript|downstream_gene_variant||||4332|LINC00662|lincRNA|||||||,-|ENSG00000261824|ENST00000588027|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00662|lincRNA|||||||,-||ENSR00001014877|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;PH=0.103;PS=0.205 GT:GL:GOF:GQ:NR:NV 1/0:-94.68,0,-149.88:5:99:86:37 0/0:0,-14.15,-176.1:0:99:48:0 19 28878659 . CA - 2070 PASS Source=Platypus;CSQ=-|ENSG00000267320|ENST00000591926|Transcript|upstream_gene_variant||||1581|AC005780.1|lincRNA|||||||,-|ENSG00000267320|ENST00000592311|Transcript|upstream_gene_variant||||1574|AC005780.1|lincRNA|YES||||||,-|ENSG00000267320|ENST00000587140|Transcript|upstream_gene_variant||||1548|AC005780.1|lincRNA|||||||;GR=0.618;PH=0.579;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-77.01,0,-59.81:1:99:47:27 0/0:0,-13.91,-170.9:1:99:48:0 19 29232177 rs12460203 A G 906 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.149;PH=-1.066;PS=0.015;REPMASK=LINE;UK10K=3267/7562;WGS500=236;1000G=0.248403 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.21,-158.4:3:99:45:0 0/1:-86.16,0,-83.56:12:99:56:29 19 29850069 . G A 401 PASS Source=Platypus;CSQ=A|ENSG00000264515|ENST00000582581|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-525D6.1|lincRNA|YES||||||;GR=0.149;PH=0.192;PS=0.229;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-73.94,0,-193.44:0:99:63:17 1/1:-227.3,-14.15,0:1:99:59:43 19 30202962 . GTGA - 439 PASS Source=Platypus;CSQ=-|ENSG00000131943|ENST00000591243|Transcript|upstream_gene_variant||||3415|C19orf12|protein_coding|||||||,-|ENSG00000131943|ENST00000392276|Transcript|intron_variant&feature_truncation|||||C19orf12|protein_coding|||||||,-|ENSG00000131943|ENST00000392278|Transcript|intron_variant&feature_truncation|||||C19orf12|protein_coding|YES||||||,-|ENSG00000131943|ENST00000342680|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||C19orf12|nonsense_mediated_decay|||||||,-|ENSG00000131943|ENST00000392275|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||C19orf12|processed_transcript|||||||,-|ENSG00000131943|ENST00000323670|Transcript|intron_variant&feature_truncation|||||C19orf12|protein_coding|||||||,-|ENSG00000131943|ENST00000592153|Transcript|intron_variant&feature_truncation|||||C19orf12|protein_coding|||||||;GR=0.217;PH=0.292;PS=0.135;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-217.4,-17.73,0:9:99:60:60 1/0:-59.05,0,-88.95:13:99:50:20 19 30700950 . T C 1628 PASS Source=Platypus;CSQ=C||ENSR00001418671|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=-6.27;PH=-2.342;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-187,-15.61,0:28:99:53:53 1/1:-186.9,-15.65,0:26:99:53:53 19 31165495 . G A 1182 PASS Source=Platypus;CSQ=A|ENSG00000198597|ENST00000592773|Transcript|intron_variant|||||ZNF536|protein_coding|||||||;GR=-3.18;PH=-1.325;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-1,-1,-1:3:99:69,58:48,0 1/2:-1,-1,-1:1:99:53,53:23,25 19 31235323 . T C 90 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.596;PH=0.478;PS=0.007;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-10.62,-129.6:1:99:38:0 1/0:-66.06,0,-44.36:5:99:39:23 19 31264433 . T C 2442 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-1.16;PH=-0.339;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-194.5,-16.26,0:7:99:56:56 1/1:-163.3,-13.25,0:4:99:47:47 19 31299533 . A G 786 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-4.52;PH=-1.771;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-80.24,0,-86.24:17:99:54:27 1/0:-112.13,0,-85.13:4:99:66:35 19 32484860 . C T 355 PASS Source=Platypus;CSQ=T|ENSG00000267489|ENST00000590053|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-360P9.4|lincRNA|YES||||||;GR=0.418;PH=0.452;PS=0.012;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-16.2,-197:4:99:56:0 1/0:-81.69,0,-119.39:1:99:58:24 19 37793436 . T C 1167 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;PH=0.064;PS=0.009;REPMASK=Satellite;SD=0.987166 GT:GL:GOF:GQ:NR:NV 0/1:-3.33,0,-15.63:7:33:31:7 1/1:-23.8,-3.08,0:2:31:27:18 19 38820063 . T C 1354 PASS Source=Platypus;CSQ=C|ENSG00000268913|ENST00000602211|Transcript|upstream_gene_variant||||2211|AC026806.2|lincRNA|YES||||||,C|ENSG00000099337|ENST00000263372|Transcript|downstream_gene_variant||||403|KCNK6|protein_coding|YES||||||,C|ENSG00000099337|ENST00000588137|Transcript|downstream_gene_variant||||3934|KCNK6|processed_transcript|||||||;GR=-1.85;PH=-0.975;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-58.27,0,-119.37:2:99:65:25 1/0:-32.76,0,-72.36:1:99:37:12 19 42160359 . CAA - 1123 PASS Source=Platypus;CSQ=-|ENSG00000268582|ENST00000600532|Transcript|downstream_gene_variant||||3471|AC005794.1|processed_pseudogene|YES||||||;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.25,-281.7:6:99:47:0 1/0:-176.24,0,-149.34:5:99:57:30 19 42856608 . C T 462 PASS Source=Platypus;CSQ=T|ENSG00000105429|ENST00000334370|Transcript|missense_variant&splice_region_variant|3784|1050|T/M||MEGF8|protein_coding|YES|deleterious(0)|probably_damaging(0.993)||||,T|ENSG00000105429|ENST00000251268|Transcript|missense_variant&splice_region_variant|3350|1117|T/M||MEGF8|protein_coding||deleterious(0)|probably_damaging(0.999)||||,T|ENSG00000105429|ENST00000593840|Transcript|upstream_gene_variant||||340|MEGF8|retained_intron|||||||;GR=5.42;PH=2.534;PS=1;ExAC=2/121096 GT:GL:GOF:GQ:NR:NV 1/0:-83.5,0,-58.3:3:99:53:30 1/1:-142.6,-11.74,0:6:99:42:42 19 43900360 . A G 2419 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.32;PH=0.372;PS=0.042;SD=0.955907 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.28,-138:4:99:43:0 1/0:-51.06,0,-66.66:2:99:40:18 19 45995142 . C T 2282 PASS Source=Platypus;CSQ=T|ENSG00000125744|ENST00000590526|Transcript|intron_variant|||||RTN2|protein_coding|||||||,T|ENSG00000125744|ENST00000344680|Transcript|intron_variant|||||RTN2|protein_coding|||||||,T|ENSG00000125744|ENST00000587597|Transcript|intron_variant&NMD_transcript_variant|||||RTN2|nonsense_mediated_decay|||||||,T|ENSG00000213889|ENST00000401705|Transcript|intron_variant|||||PPM1N|protein_coding|||||||,T|ENSG00000125744|ENST00000593129|Transcript|upstream_gene_variant||||2781|RTN2|retained_intron|||||||,T|ENSG00000125744|ENST00000588036|Transcript|intron_variant&non_coding_transcript_variant|||||RTN2|processed_transcript|||||||,T|ENSG00000125744|ENST00000591789|Transcript|upstream_gene_variant||||2911|RTN2|retained_intron|||||||,T|ENSG00000125744|ENST00000430715|Transcript|intron_variant|||||RTN2|protein_coding|||||||,T|ENSG00000125744|ENST00000590746|Transcript|intron_variant&non_coding_transcript_variant|||||RTN2|processed_transcript|||||||,T|ENSG00000125744|ENST00000592064|Transcript|downstream_gene_variant||||2002|RTN2|retained_intron|||||||,T|ENSG00000125744|ENST00000245923|Transcript|intron_variant|||||RTN2|protein_coding|YES||||||,T|ENSG00000125744|ENST00000589628|Transcript|upstream_gene_variant||||2331|RTN2|retained_intron|||||||,T|ENSG00000125744|ENST00000589384|Transcript|downstream_gene_variant||||2671|RTN2|processed_transcript|||||||,T|ENSG00000125744|ENST00000591286|Transcript|intron_variant&NMD_transcript_variant|||||RTN2|nonsense_mediated_decay|||||||,T|ENSG00000125744|ENST00000593187|Transcript|upstream_gene_variant||||3315|RTN2|retained_intron|||||||;GR=0.875;PH=0.743;PS=0.005;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-16.26,-198.7:1:99:55:0 1/0:-66.38,0,-85.88:8:99:52:24 19 46394032 . A G 191 PASS Source=Platypus;CSQ=G|ENSG00000176182|ENST00000322217|Transcript|missense_variant|1136|350|V/A||MYPOP|protein_coding|YES|deleterious(0.02)|probably_damaging(0.935)||||,G|ENSG00000170604|ENST00000302165|Transcript|upstream_gene_variant||||4656|IRF2BP1|protein_coding|YES||||||;GR=1.62;PH=1.604;PS=0.925 GT:GL:GOF:GQ:NR:NV 1/0:-99.84,0,-300:1:99:253:24 1/0:-212.82,0,-300:5:99:174:36 19 48039996 . C T 2785 PASS Source=Platypus;CSQ=T|ENSG00000118156|ENST00000314121|Transcript|intron_variant|||||ZNF541|protein_coding|YES||||||,T|ENSG00000118156|ENST00000263351|Transcript|intron_variant|||||ZNF541|protein_coding|||||||,T|ENSG00000118156|ENST00000487275|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF541|processed_transcript|||||||,T|ENSG00000118156|ENST00000595558|Transcript|intron_variant|||||ZNF541|protein_coding|||||||,T|ENSG00000118156|ENST00000448976|Transcript|intron_variant|||||ZNF541|protein_coding|||||||,T|ENSG00000118156|ENST00000391901|Transcript|intron_variant|||||ZNF541|protein_coding|||||||;PH=-1.371;PS=0.033;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-40.86,0,-74.26:3:99:41:18 0/0:0,-7.53,-95:5:75:29:0 19 50181803 . TTG - 106 PASS Source=Platypus;CSQ=-|ENSG00000126457|ENST00000526224|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126453|ENST00000246785|Transcript|downstream_gene_variant||||4630|BCL2L12|protein_coding|YES||||||,-|ENSG00000126457|ENST00000525915|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PRMT1|retained_intron|||||||,-|ENSG00000126457|ENST00000528623|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126457|ENST00000525616|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PRMT1|retained_intron|||||||,-|ENSG00000126453|ENST00000594157|Transcript|downstream_gene_variant||||4630|BCL2L12|protein_coding|||||||,-|ENSG00000126457|ENST00000524771|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126453|ENST00000598979|Transcript|downstream_gene_variant||||4630|BCL2L12|nonsense_mediated_decay|||||||,-|ENSG00000126457|ENST00000391851|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126457|ENST00000534465|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126457|ENST00000529836|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126457|ENST00000534280|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PRMT1|nonsense_mediated_decay|||||||,-|ENSG00000126457|ENST00000532489|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126453|ENST00000600947|Transcript|downstream_gene_variant||||4630|BCL2L12|protein_coding|||||||,-|ENSG00000126453|ENST00000598306|Transcript|downstream_gene_variant||||4630|BCL2L12|protein_coding|||||||,-|ENSG00000126457|ENST00000534676|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PRMT1|retained_intron|||||||,-|ENSG00000126457|ENST00000454376|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|YES||||||,-|ENSG00000126457|ENST00000527382|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000264413|ENST00000581740|Transcript|upstream_gene_variant||||3523|AC011495.1|miRNA|YES||||||,-|ENSG00000126453|ENST00000246784|Transcript|downstream_gene_variant||||4631|BCL2L12|protein_coding|||||||,-|ENSG00000126457|ENST00000529284|Transcript|intron_variant&feature_truncation|||||PRMT1|protein_coding|||||||,-|ENSG00000126457|ENST00000527412|Transcript|upstream_gene_variant||||1227|PRMT1|protein_coding|||||||,-|ENSG00000126453|ENST00000594793|Transcript|downstream_gene_variant||||4631|BCL2L12|processed_transcript|||||||,-|ENSG00000126453|ENST00000441864|Transcript|downstream_gene_variant||||4687|BCL2L12|protein_coding|||||||,-||ENSR00000348238|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.663;PH=0.081;PS=0.291 GT:GL:GOF:GQ:NR:NV 0/1:-87.87,0,-79.97:2:99:54:29 1/1:-170.9,-14.12,0:1:99:48:48 19 52285783 . AT - 2742 PASS Source=Platypus;CSQ=-|ENSG00000171051|ENST00000594900|Transcript|intron_variant&feature_truncation|||||FPR1|protein_coding|||||||;GR=0.137;PH=0.249;PS=0.021;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-18.36,-208.8:1:99:65:0 0/1:-77.54,0,-88.84:1:99:57:26 19 52849534 rs541275533 C T 1876 PASS Source=Platypus;CSQ=T|ENSG00000167554|ENST00000327920|Transcript|intron_variant|||||ZNF610|protein_coding|||||||,T|ENSG00000167554|ENST00000594919|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF610|retained_intron|||||||,T|ENSG00000167554|ENST00000321287|Transcript|intron_variant|||||ZNF610|protein_coding|||||||,T|ENSG00000269535|ENST00000594379|Transcript|upstream_gene_variant||||1052|CTD-2525I3.6|antisense|YES||||||,T|ENSG00000167554|ENST00000403906|Transcript|intron_variant|||||ZNF610|protein_coding|YES||||||,T|ENSG00000167554|ENST00000601151|Transcript|intron_variant|||||ZNF610|protein_coding|||||||,T|ENSG00000167554|ENST00000593698|Transcript|intron_variant|||||ZNF610|protein_coding|||||||,T|ENSG00000167554|ENST00000599508|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF610|retained_intron|||||||;GR=0.149;PH=0.192;PS=0.058;REPMASK=SINE;1000G=0.000199681 GT:GL:GOF:GQ:NR:NV 0/1:-59.25,0,-93.35:5:99:52:21 0/0:0,-15.95,-196.8:0:99:54:0 19 53061123 . C T 1254 PASS Source=Platypus;CSQ=T|ENSG00000198482|ENST00000461321|Transcript|downstream_gene_variant||||4434|ZNF808|protein_coding|||||||,T|ENSG00000198482|ENST00000486474|Transcript|downstream_gene_variant||||4439|ZNF808|protein_coding|||||||,T|ENSG00000198482|ENST00000359798|Transcript|downstream_gene_variant||||1534|ZNF808|protein_coding|YES||||||,T|ENSG00000167562|ENST00000478039|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF701|processed_transcript|||||||,T|ENSG00000198482|ENST00000465448|Transcript|downstream_gene_variant||||4414|ZNF808|protein_coding|||||||,T|ENSG00000198482|ENST00000461779|Transcript|downstream_gene_variant||||4704|ZNF808|protein_coding|||||||,T|ENSG00000198482|ENST00000487863|Transcript|intron_variant&NMD_transcript_variant|||||ZNF808|nonsense_mediated_decay|||||||;GR=-0.442;PH=-0.09;PS=0.003;SD=0.912296 GT:GL:GOF:GQ:NR:NV 0/0:0,-14.73,-174.8:3:99:51:0 1/0:-53.71,0,-77.81:1:99:47:19 19 53802628 . T C 1198 PASS Source=Platypus;CSQ=C|ENSG00000269118|ENST00000597191|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|1050||||FAM90A28P|transcribed_unprocessed_pseudogene|YES||||||,C|ENSG00000269118|ENST00000596881|Transcript|downstream_gene_variant||||2747|FAM90A28P|processed_transcript|||||||;GR=-4.03;PH=-2.227;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.91,-232:1:99:65:0 0/1:-75.34,0,-97.74:0:99:57:25 19 54927313 . T C 1136 PASS Source=Platypus;CSQ=C|ENSG00000167614|ENST00000472198|Transcript|upstream_gene_variant||||3057|TTYH1|nonsense_mediated_decay|||||||,C|ENSG00000167614|ENST00000391739|Transcript|intron_variant|||||TTYH1|protein_coding|||||||,C|ENSG00000167614|ENST00000462769|Transcript|upstream_gene_variant||||2123|TTYH1|processed_transcript|||||||,C|ENSG00000167614|ENST00000376531|Transcript|intron_variant|||||TTYH1|protein_coding|YES||||||,C|ENSG00000167614|ENST00000461302|Transcript|upstream_gene_variant||||4529|TTYH1|processed_transcript|||||||,C|ENSG00000167614|ENST00000423529|Transcript|intron_variant|||||TTYH1|protein_coding|||||||,C|ENSG00000167614|ENST00000478036|Transcript|upstream_gene_variant||||2250|TTYH1|processed_transcript|||||||,C|ENSG00000167614|ENST00000487134|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|251||||TTYH1|retained_intron|||||||,C|ENSG00000167614|ENST00000376530|Transcript|intron_variant|||||TTYH1|protein_coding|||||||,C|ENSG00000167614|ENST00000445095|Transcript|intron_variant|||||TTYH1|protein_coding|||||||,C|ENSG00000167614|ENST00000301194|Transcript|intron_variant|||||TTYH1|protein_coding|||||||,C|ENSG00000167614|ENST00000425969|Transcript|intron_variant&NMD_transcript_variant|||||TTYH1|nonsense_mediated_decay|||||||,C|ENSG00000167614|ENST00000476757|Transcript|upstream_gene_variant||||4560|TTYH1|processed_transcript|||||||,C|ENSG00000167614|ENST00000462757|Transcript|intron_variant&non_coding_transcript_variant|||||TTYH1|processed_transcript|||||||,C||ENSR00001015078|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;PH=0.141;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/1:-217.4,-17.76,0:26:99:62:62 1/0:-87.54,0,-82.64:1:99:60:29 19 55246162 . T C 1902 PASS Source=Platypus;CSQ=C|ENSG00000189013|ENST00000396284|Transcript|intron_variant|||||KIR2DL4|protein_coding|||||||,C|ENSG00000167633|ENST00000541392|Transcript|intron_variant|||||KIR3DL1|protein_coding|||||||,C|ENSG00000167633|ENST00000538269|Transcript|intron_variant|||||KIR3DL1|protein_coding|||||||,C|ENSG00000167633|ENST00000402254|Transcript|intron_variant|||||KIR3DL1|protein_coding|||||||,C|ENSG00000242019|ENST00000291860|Transcript|intron_variant|||||KIR3DL3|protein_coding|YES||||||,C|ENSG00000243772|ENST00000434419|Transcript|upstream_gene_variant||||3820|KIR2DL3|protein_coding|||||||,C|ENSG00000215765|ENST00000400864|Transcript|intron_variant&non_coding_transcript_variant|||||CTB-61M7.1|processed_transcript|YES||||||,C|ENSG00000243772|ENST00000342376|Transcript|upstream_gene_variant||||3818|KIR2DL3|protein_coding|YES||||||;GR=0.149;PH=0.166;PS=0.006;REPMASK=LTR;SD=0.982462 GT:GL:GOF:GQ:NR:NV 0/0:0,-4.82,-88.4:9:48:20:0 0/1:-70.96,0,-86.16:30:99:38:18 19 55545438 . A G 2589 PASS Source=Platypus;CSQ=G|ENSG00000088053|ENST00000417454|Transcript|intron_variant|||||GP6|protein_coding|||||||,G|ENSG00000088053|ENST00000310373|Transcript|intron_variant|||||GP6|protein_coding|YES||||||,G|ENSG00000088053|ENST00000468239|Transcript|upstream_gene_variant||||1205|GP6|protein_coding|||||||,G|ENSG00000088053|ENST00000333884|Transcript|intron_variant|||||GP6|protein_coding|||||||,G|ENSG00000267265|ENST00000586961|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-550B14.7|antisense|||||||,G|ENSG00000267149|ENST00000585492|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-550B14.6|processed_transcript|YES||||||,G|ENSG00000267265|ENST00000586845|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-550B14.7|antisense|||||||,G|ENSG00000267265|ENST00000593060|Transcript|intron_variant&non_coding_transcript_variant|||||CTC-550B14.7|antisense|YES||||||;GR=0.122;PH=0.166;PS=0.021;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/1:-82.52,0,-89.82:2:99:62:29 0/0:0,-10.73,-132.9:6:99:41:0 19 57051579 . TG - 1402 PASS Source=Platypus;CSQ=-|ENSG00000267224|ENST00000592125|Transcript|downstream_gene_variant||||4447|AC005498.4|lincRNA|YES||||||,-|ENSG00000267421|ENST00000587920|Transcript|upstream_gene_variant||||1835|AC005498.3|lincRNA|||||||,-|ENSG00000267421|ENST00000601933|Transcript|upstream_gene_variant||||1895|AC005498.3|lincRNA|||||||,-|ENSG00000196867|ENST00000589836|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ZFP28|nonsense_mediated_decay|||||||,-|ENSG00000267421|ENST00000590613|Transcript|upstream_gene_variant||||1635|AC005498.3|lincRNA|||||||,-|ENSG00000196867|ENST00000591844|Transcript|intron_variant&feature_truncation|||||ZFP28|protein_coding|||||||,-|ENSG00000196867|ENST00000301318|Transcript|intron_variant&feature_truncation|||||ZFP28|protein_coding|YES||||||,-|ENSG00000196867|ENST00000594386|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ZFP28|processed_transcript|||||||,-|ENSG00000267421|ENST00000590579|Transcript|upstream_gene_variant||||1792|AC005498.3|lincRNA|||||||,-|ENSG00000267421|ENST00000593218|Transcript|upstream_gene_variant||||1779|AC005498.3|lincRNA|YES||||||;GR=-1.45;PH=-0.529;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-102.2,-6.45,0:6:64:23:21 1/1:-286.6,-19.17,0:3:99:66:55 19 57683078 . G A 2780 PASS Source=Platypus;CSQ=A|ENSG00000268379|ENST00000594883|Transcript|upstream_gene_variant||||3523|CTC-360J11.4|processed_pseudogene|YES||||||,A|ENSG00000258873|ENST00000554048|Transcript|upstream_gene_variant||||4267|DUXA|protein_coding|YES||||||,A||ENSR00000045601|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.31;PH=-0.326;PS=0.034 GT:GL:GOF:GQ:NR:NV 0/1:-38.61,0,-119.41:4:99:28:6 0/1:-25.97,0,-138.27:3:99:29:5 19 58662922 . CG - 15 PASS Source=Platypus;CSQ=-|ENSG00000181894|ENST00000598312|Transcript|upstream_gene_variant||||777|ZNF329|protein_coding|YES||||||,-|ENSG00000181894|ENST00000500161|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||ZNF329|nonsense_mediated_decay|||||||,-|ENSG00000181894|ENST00000601887|Transcript|intron_variant&feature_truncation|||||ZNF329|protein_coding|||||||,-|ENSG00000181894|ENST00000597186|Transcript|upstream_gene_variant||||768|ZNF329|nonsense_mediated_decay|||||||;GR=0.158;PH=0.202;PS=0.044;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-210.8,-17.44,0:3:99:60:60 0/0:0,-13.55,-168.7:6:99:49:0 19 58666745 . C T 2315 PASS Source=Platypus;CSQ=T|ENSG00000181894|ENST00000598312|Transcript|upstream_gene_variant||||4600|ZNF329|protein_coding|YES||||||,T|ENSG00000181894|ENST00000500161|Transcript|upstream_gene_variant||||268|ZNF329|nonsense_mediated_decay|||||||,T|ENSG00000181894|ENST00000601887|Transcript|upstream_gene_variant||||311|ZNF329|protein_coding|||||||,T|ENSG00000181894|ENST00000597186|Transcript|upstream_gene_variant||||4591|ZNF329|nonsense_mediated_decay|||||||,T||ENSR00000349268|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.03;PH=0.865;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.86,-208.5:1:99:57:0 0/1:-62.55,0,-74.95:1:99:49:23 2 7148401 . G A 1385 PASS Source=Platypus;CSQ=A|ENSG00000151692|ENST00000433456|Transcript|intron_variant|||||RNF144A|protein_coding|||||||,A|ENSG00000151692|ENST00000471060|Transcript|intron_variant&non_coding_transcript_variant|||||RNF144A|retained_intron|||||||,A|ENSG00000151692|ENST00000416587|Transcript|intron_variant|||||RNF144A|protein_coding|||||||,A|ENSG00000151692|ENST00000432850|Transcript|intron_variant|||||RNF144A|protein_coding|||||||,A|ENSG00000151692|ENST00000320892|Transcript|intron_variant|||||RNF144A|protein_coding|YES||||||,A|ENSG00000151692|ENST00000467276|Transcript|intron_variant&non_coding_transcript_variant|||||RNF144A|processed_transcript|||||||,A|ENSG00000151692|ENST00000480970|Transcript|intron_variant&non_coding_transcript_variant|||||RNF144A|processed_transcript|||||||,A||ENSR00001539102|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.02;PH=0.349;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-103.42,0,-69.62:2:99:54:31 1/0:-61.67,0,-65.37:6:99:36:17 2 10695607 . ATGG - 951 PASS Source=Platypus;CSQ=-||ENSR00000585153|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=-7.46;PH=-1.735;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.46,-135.7:3:99:66:0 0/1:-56.95,0,-47.05:6:99:54:19 2 15759098 . A G 399 PASS Source=Platypus;CSQ=G|ENSG00000079785|ENST00000478695|Transcript|upstream_gene_variant||||4559|DDX1|retained_intron|||||||,G|ENSG00000079785|ENST00000470674|Transcript|upstream_gene_variant||||2118|DDX1|retained_intron|||||||,G|ENSG00000079785|ENST00000381341|Transcript|intron_variant|||||DDX1|protein_coding|YES||||||,G|ENSG00000079785|ENST00000459706|Transcript|intron_variant&non_coding_transcript_variant|||||DDX1|retained_intron|||||||,G|ENSG00000079785|ENST00000233084|Transcript|intron_variant|||||DDX1|protein_coding|||||||;GR=0.235;PH=0.263;PS=0.034;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-91.44,0,-70.54:2:99:58:31 0/0:0,-15.05,-186.8:2:99:55:0 2 16991723 . T C 2038 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-3.4;PH=-0.851;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-66.46,0,-109.26:5:99:63:24 1/1:-197.1,-16.19,0:11:99:56:56 2 18759630 . CC - 273 PASS Source=Platypus;CSQ=-|ENSG00000185013|ENST00000359846|Transcript|intron_variant&feature_truncation|||||NT5C1B|protein_coding|YES||||||,-|ENSG00000185013|ENST00000406971|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NT5C1B|nonsense_mediated_decay|||||||,-|ENSG00000185013|ENST00000304081|Transcript|intron_variant&feature_truncation|||||NT5C1B|protein_coding|||||||,-|ENSG00000185013|ENST00000600945|Transcript|intron_variant&feature_truncation|||||NT5C1B|protein_coding|||||||,-|ENSG00000250741|ENST00000532967|Transcript|intron_variant&feature_truncation|||||NT5C1B-RDH14|protein_coding|YES||||||,-|ENSG00000185013|ENST00000418427|Transcript|intron_variant&feature_truncation|||||NT5C1B|protein_coding|||||||,-|ENSG00000250741|ENST00000444297|Transcript|intron_variant&feature_truncation|||||NT5C1B-RDH14|protein_coding|||||||;GR=0.225;PH=0.3;PS=0.254;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-89.85,0,-46.45:8:99:50:31 0/0:0,-13.46,-146.3:4:99:50:0 2 25604442 . G A 1013 PASS Source=Platypus;CSQ=A|ENSG00000138101|ENST00000489949|Transcript|downstream_gene_variant||||2110|DTNB|retained_intron|||||||,A|ENSG00000138101|ENST00000497476|Transcript|intron_variant&non_coding_transcript_variant|||||DTNB|processed_transcript|||||||,A|ENSG00000138101|ENST00000398951|Transcript|intron_variant&NMD_transcript_variant|||||DTNB|nonsense_mediated_decay|||||||,A|ENSG00000138101|ENST00000496972|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000407186|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000356599|Transcript|intron_variant&NMD_transcript_variant|||||DTNB|nonsense_mediated_decay|||||||,A|ENSG00000138101|ENST00000406818|Transcript|intron_variant|||||DTNB|protein_coding|YES||||||,A|ENSG00000138101|ENST00000488457|Transcript|upstream_gene_variant||||1660|DTNB|retained_intron|||||||,A|ENSG00000138101|ENST00000407038|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000405222|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000545439|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000404103|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000407661|Transcript|intron_variant|||||DTNB|protein_coding|||||||,A|ENSG00000138101|ENST00000288642|Transcript|intron_variant|||||DTNB|protein_coding|||||||;GR=0.235;PH=0.308;PS=0.28;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-46.92,0,-17.72:5:99:23:15 0/0:0,-5.12,-65.2:4:51:18:0 2 26519919 . T C 2050 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.256;PH=-1.555;PS=0.02;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-221.5,-1.81,0:2:18:13:3 0/1:-98.89,0,-91.29:10:99:16:2 2 29314244 . GAGG - 420 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.42;PH=0.375;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-141,0,-100.57:2:99:53:30 0/0:0,-17.46,-265.6:1:99:60:0 2 44358065 . A G 2454 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-4.13;PH=-0.77;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.62,-144.3:2:99:47:0 0/1:-59.26,0,-59.46:21:99:45:21 2 45218104 . A G 1365 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-1.61;PH=-0.36;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-98.96,0,-95.56:0:99:68:35 0/0:0,-14.15,-172:4:99:49:0 2 52840038 . TGAG - 1534 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-5.5;PH=-1.317;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-73.75,0,-96.55:0:99:58:27 0/1:-88.15,0,-66.25:1:99:50:28 2 53854754 . AG - 2857 PASS Source=Platypus;CSQ=-|ENSG00000115239|ENST00000406053|Transcript|intron_variant&feature_truncation|||||GPR75-ASB3|protein_coding|||||||;GR=0.79;PH=0.597;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-178.7,-15.56,0:135:99:58:58 1/1:-152.6,-12.92,0:114:99:48:48 2 64697866 . T C 1224 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-5.55;PH=-0.657;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-11.5,-0.6,0:40:7:3:3 1/1:-18.2,-1.2,0:32:12:5:5 2 69734168 . GGAC - 2969 PASS Source=Platypus;CSQ=-|ENSG00000115977|ENST00000406297|Transcript|intron_variant&feature_truncation|||||AAK1|protein_coding|||||||,-|ENSG00000115977|ENST00000409085|Transcript|intron_variant&feature_truncation|||||AAK1|protein_coding|YES||||||,-|ENSG00000115977|ENST00000409068|Transcript|intron_variant&feature_truncation|||||AAK1|protein_coding|||||||,-|ENSG00000115977|ENST00000489327|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AAK1|retained_intron|||||||;GR=0.687;PH=0.138;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-188.9:2:99:55:0 1/0:-48.96,0,-74.86:1:99:43:18 2 69892858 . AAA - 788 PASS Source=Platypus;CSQ=-|ENSG00000238708|ENST00000459058|Transcript|upstream_gene_variant||||1631|snoU13|snoRNA|YES||||||,-|ENSG00000196975|ENST00000418066|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ANXA4|processed_transcript|||||||,-|ENSG00000115977|ENST00000461002|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AAK1|processed_transcript|||||||;GR=0.128;PH=0.243;PS=0.185;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-213.8:3:99:63:0 1/0:-76.76,0,-90.76:1:99:60:29 2 75187003 . CGC - 2381 PASS Source=Platypus;CSQ=-|ENSG00000115350|ENST00000459636|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||POLE4|processed_transcript|||||||,-|ENSG00000115350|ENST00000483063|Transcript|intron_variant&feature_truncation|||||POLE4|protein_coding|YES||||||,-|ENSG00000115350|ENST00000473023|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||POLE4|retained_intron|||||||,-|ENSG00000115350|ENST00000233699|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||POLE4|processed_transcript|||||||,-|ENSG00000115350|ENST00000465242|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||POLE4|processed_transcript|||||||,-|ENSG00000115350|ENST00000485527|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||POLE4|retained_intron|||||||;GR=2.23;PH=0.444;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-209.5,-17.14,0:3:99:58:58 0/1:-110.34,0,-85.14:2:99:63:35 2 81852219 . T C 2154 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;PH=0.103;PS=0.001;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 1/1:-96.5,-7.8,0:44:78:35:27 1/1:-119.4,-9.63,0:48:96:35:34 2 95408169 . GT - 1905 PASS Source=Platypus;CSQ=-|ENSG00000213355|ENST00000421872|Transcript|downstream_gene_variant||||4175|CNN2P8|processed_pseudogene|YES||||||;GR=0.109;PH=0.181;PS=0.049;SD=0.966913 GT:GL:GOF:GQ:NR:NV 1/1:-227.5,-18.6,0:7:99:64:64 0/1:-71.45,0,-84.45:2:99:51:23 2 97463811 . AC - 475 PASS Source=Platypus;CSQ=-|ENSG00000158158|ENST00000493384|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CNNM4|processed_transcript|||||||,-|ENSG00000158158|ENST00000540067|Transcript|intron_variant&feature_truncation|||||CNNM4|protein_coding|||||||,-|ENSG00000264157|ENST00000583925|Transcript|upstream_gene_variant||||203|MIR3127|miRNA|YES||||||,-|ENSG00000158158|ENST00000377075|Transcript|intron_variant&feature_truncation|||||CNNM4|protein_coding|YES||||||,-|ENSG00000158158|ENST00000496186|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CNNM4|processed_transcript|||||||,-|ENSG00000158158|ENST00000482716|Transcript|downstream_gene_variant||||464|CNNM4|processed_transcript|||||||;GR=-0.598;PH=-0.292;PS=0.026;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-64.31,0,-80.91:1:99:58:24 1/0:-60.95,0,-70.15:2:99:51:24 2 104696424 . T C 2973 PASS Source=Platypus;CSQ=C|ENSG00000256637|ENST00000545549|Transcript|downstream_gene_variant||||2443|RP11-76I14.1|lincRNA|||||||,C|ENSG00000256637|ENST00000544869|Transcript|downstream_gene_variant||||2188|RP11-76I14.1|lincRNA|||||||,C|ENSG00000256637|ENST00000537492|Transcript|downstream_gene_variant||||2362|RP11-76I14.1|lincRNA|||||||;GR=0.149;PH=0.166;PS=0.235;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-117.39,0,-94.29:16:99:62:33 1/0:-62.69,0,-80.99:12:99:43:20 2 107621181 . CT - 2262 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.08;PH=-0.779;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.65,-191.4:4:99:55:0 0/1:-98.34,0,-84.54:0:99:62:33 2 117942632 . A G 22 PASS Source=Platypus;CSQ=G|ENSG00000227291|ENST00000440211|Transcript|upstream_gene_variant||||3494|AC092170.1|processed_pseudogene|YES||||||;PH=0.056;PS=0.353;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-51.25,0,-96.65:3:99:53:22 1/0:-105.64,0,-56.84:5:99:55:35 2 119805041 . TTT - 2134 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.118;PH=0.165;PS=0.076;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-211.5,-17.76,0:1:99:60:60 1/1:-204.3,-16.81,0:1:99:57:57 2 125497634 . T C 2412 PASS Source=Platypus;CSQ=C|ENSG00000155052|ENST00000431078|Transcript|intron_variant|||||CNTNAP5|protein_coding|YES||||||;GR=0.674;PH=0.179;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-78.28,0,-70.88:4:99:53:28 0/0:0,-9.03,-109:2:90:31:0 2 135377709 . T C 2963 PASS Source=Platypus;CSQ=C|ENSG00000152128|ENST00000281924|Transcript|intron_variant|||||TMEM163|protein_coding|YES||||||;PH=0.103;PS=0.292;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-300,0,-300:151:99:53:3 1/0:-300,0,-300:147:99:48:9 2 141928946 . A G 1876 PASS Source=Platypus;CSQ=G|ENSG00000168702|ENST00000389484|Transcript|intron_variant|||||LRP1B|protein_coding|YES||||||,G|ENSG00000252015|ENST00000516206|Transcript|upstream_gene_variant||||4020|RNU6-904P|snRNA|YES||||||,G|ENSG00000168702|ENST00000434794|Transcript|intron_variant|||||LRP1B|protein_coding|||||||;GR=-1.28;PH=-0.342;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-67.35,0,-67.55:1:99:49:25 0/0:0,-9.33,-113.8:5:93:36:0 2 142413488 . T C 1976 PASS Source=Platypus;CSQ=C|ENSG00000168702|ENST00000389484|Transcript|intron_variant|||||LRP1B|protein_coding|YES||||||,C|ENSG00000168702|ENST00000434794|Transcript|intron_variant|||||LRP1B|protein_coding|||||||;GR=-3.11;PH=-0.631;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.42,-210.8:4:99:66:0 0/1:-68.45,0,-68.95:6:99:52:25 2 145719703 . GCCA - 1859 PASS Source=Platypus;CSQ=-|ENSG00000226674|ENST00000597670|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000600064|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000596230|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000594626|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000596540|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000445791|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|YES||||||,-|ENSG00000226674|ENST00000600679|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000598248|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000597655|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000451774|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000594471|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000451027|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000595686|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000598659|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000597469|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000599187|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000597893|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000601277|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000596589|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||,-|ENSG00000226674|ENST00000599072|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TEX41|lincRNA|||||||;GR=-1.34;PH=-0.365;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-1,-1,-1:23:99:216,214:59,20 0/2:-1,-1,-1:18:61:186,187:33,29 2 151421297 . A G 442 PASS Source=Platypus;CSQ=G|ENSG00000236049|ENST00000441356|Transcript|intron_variant&non_coding_transcript_variant|||||AC104777.2|lincRNA|YES||||||,G|ENSG00000237220|ENST00000416350|Transcript|upstream_gene_variant||||1351|AC104777.3|lincRNA|YES||||||;GR=-2.21;PH=-0.475;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/0:-78.46,0,-164.96:1:99:38:12 0/0:0,-17.76,-300:1:99:61:0 2 176995495 . C T 1044 PASS Source=Platypus;CSQ=T|ENSG00000175879|ENST00000548663|Transcript|intron_variant|||||HOXD8|protein_coding|||||||,T|ENSG00000175879|ENST00000544999|Transcript|missense_variant|727|134|A/V||HOXD8|protein_coding||tolerated(0.08)|benign(0.194)||||,T|ENSG00000175879|ENST00000450510|Transcript|missense_variant|411|134|A/V||HOXD8|protein_coding||tolerated(0.08)|benign(0.194)||||,T|ENSG00000175879|ENST00000429017|Transcript|intron_variant|||||HOXD8|protein_coding|||||||,T|ENSG00000237380|ENST00000426965|Transcript|downstream_gene_variant||||3839|HOXD-AS2|antisense|||||||,T|ENSG00000237380|ENST00000440016|Transcript|intron_variant&non_coding_transcript_variant|||||HOXD-AS2|antisense|YES||||||,T|ENSG00000175879|ENST00000313173|Transcript|missense_variant|1028|134|A/V||HOXD8|protein_coding|YES|tolerated(0.08)|benign(0.31)||||,T||ENSR00000124608|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=4.27;PH=2.069;PS=1;WGS500=2 GT:GL:GOF:GQ:NR:NV 0/1:-45.98,0,-67.48:3:99:50:23 0/1:-63.15,0,-74.15:4:99:52:24 2 179414205 . A G 1005 PASS Source=Platypus;CSQ=G|ENSG00000237298|ENST00000592630|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000592689|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000438095|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000590807|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000586707|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000270277|ENST00000603415|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|595||||RP11-65L3.2|antisense|YES||||||,G|ENSG00000237298|ENST00000586831|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000585451|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000155657|ENST00000359218|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|||||||,G|ENSG00000237298|ENST00000592600|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000155657|ENST00000591111|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|||||||,G|ENSG00000155657|ENST00000589042|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|YES||||||,G|ENSG00000237298|ENST00000592750|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000419746|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|YES||||||,G|ENSG00000237298|ENST00000456053|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000586452|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000237298|ENST00000591332|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000155657|ENST00000342175|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|||||||,G|ENSG00000155657|ENST00000342992|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|||||||,G|ENSG00000237298|ENST00000590932|Transcript|intron_variant&non_coding_transcript_variant|||||TTN-AS1|antisense|||||||,G|ENSG00000155657|ENST00000460472|Transcript|splice_region_variant&intron_variant|||||TTN|protein_coding|||||||;GR=0.403;PH=-0.087;PS=0.002;WGS500=2 GT:GL:GOF:GQ:NR:NV 0/1:-58.15,0,-89.95:2:99:49:20 0/1:-47.07,0,-50.07:1:99:35:19 2 179665172 . G T 1658 PASS Source=Platypus;CSQ=T|ENSG00000155657|ENST00000412264|Transcript|downstream_gene_variant||||1842|TTN|protein_coding|||||||,T|ENSG00000155657|ENST00000360870|Transcript|missense_variant|756|178|A/D||TTN|protein_coding||deleterious(0)|probably_damaging(0.999)||||,T|ENSG00000155657|ENST00000342992|Transcript|missense_variant|756|178|A/D||TTN|protein_coding|||||||,T|ENSG00000155657|ENST00000342175|Transcript|missense_variant|758|178|A/D||TTN|protein_coding|||unknown(0)||||,T|ENSG00000155657|ENST00000359218|Transcript|missense_variant|758|178|A/D||TTN|protein_coding|||||||,T|ENSG00000155657|ENST00000470257|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|743||||TTN|retained_intron|||||||,T|ENSG00000155657|ENST00000589042|Transcript|missense_variant|758|178|A/D||TTN|protein_coding|YES||||||,T|ENSG00000155657|ENST00000591111|Transcript|missense_variant|758|178|A/D||TTN|protein_coding|||||||,T|ENSG00000155657|ENST00000460472|Transcript|missense_variant|758|178|A/D||TTN|protein_coding|||||||;GR=5.16;PH=1.551;PS=0.993;WGS500=2 GT:GL:GOF:GQ:NR:NV 0/1:-107.64,0,-81.44:5:99:67:38 0/1:-62.87,0,-84.37:4:99:51:22 2 180629854 . GG - 2502 PASS Source=Platypus;CSQ=-|ENSG00000144331|ENST00000438871|Transcript|downstream_gene_variant||||4534|ZNF385B|protein_coding|||||||,-|ENSG00000144331|ENST00000451732|Transcript|downstream_gene_variant||||4402|ZNF385B|protein_coding|||||||,-|ENSG00000144331|ENST00000410066|Transcript|intron_variant&feature_truncation|||||ZNF385B|protein_coding|YES||||||;GR=1.18;PH=0.947;PS=0.186;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-17.16,-209.6:2:99:57:0 1/0:-110.58,0,-78.68:2:99:65:36 2 189957043 . A G 692 PASS Source=Platypus;CSQ=G|ENSG00000228073|ENST00000419029|Transcript|upstream_gene_variant||||2746|AC133106.2|antisense|YES||||||,G|ENSG00000204262|ENST00000374866|Transcript|missense_variant|835|187|L/S||COL5A2|protein_coding|YES|tolerated(0.38)|possibly_damaging(0.67)||||;GR=5.88;PH=2.243;PS=1 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.44,-203.3:1:99:60:0 0/1:-83.65,0,-61.15:1:99:47:28 2 190763689 . T C 1909 PASS Source=Platypus;CSQ=C|ENSG00000187699|ENST00000495546|Transcript|intron_variant&non_coding_transcript_variant|||||C2orf88|processed_transcript|||||||,C|ENSG00000187699|ENST00000478197|Transcript|intron_variant&non_coding_transcript_variant|||||C2orf88|processed_transcript|||||||;GR=1.41;PH=0.903;PS=0.007;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-85.98,0,-91.98:19:99:63:32 0/0:0,-15.91,-190.7:19:99:54:0 2 191807746 . GC - 1600 PASS Source=Platypus;CSQ=-|ENSG00000115419|ENST00000412247|Transcript|intron_variant&feature_truncation|||||GLS|protein_coding|||||||,-|ENSG00000115419|ENST00000457316|Transcript|intron_variant&feature_truncation|||||GLS|protein_coding|||||||,-|ENSG00000115419|ENST00000320717|Transcript|intron_variant&feature_truncation|||||GLS|protein_coding|YES||||||,-|ENSG00000115419|ENST00000409428|Transcript|intron_variant&feature_truncation|||||GLS|protein_coding|||||||;GR=-1.23;PH=-0.328;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-228.4,-20.29,0:2:99:72:72 0/1:-67.15,0,-73.45:5:99:49:22 2 198190425 . C T 269 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.367;PH=0.475;PS=0.024;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-58.45,0,-103.15:12:99:54:22 1/0:-61.35,0,-84.55:9:99:49:21 2 208320060 . C T 1138 PASS Source=Platypus;CSQ=T|ENSG00000223725|ENST00000412387|Transcript|intron_variant&non_coding_transcript_variant|||||AC007879.5|antisense|||||||,T|ENSG00000223725|ENST00000418850|Transcript|intron_variant&non_coding_transcript_variant|||||AC007879.5|antisense|YES||||||;GR=0.109;PH=0.181;PS=0.42;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-160.5,-13.43,0:10:99:47:47 0/1:-55.06,0,-51.76:12:99:35:18 2 212164801 . C T 1632 PASS Source=Platypus;CSQ=T|ENSG00000231017|ENST00000413068|Transcript|upstream_gene_variant||||887|AC013404.1|processed_pseudogene|YES||||||;GR=0.225;PH=0.3;PS=0.074;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-184.1,-15.65,0:2:99:55:55 1/1:-204.6,-16.26,0:2:99:56:56 2 219731478 . G A 1224 PASS Source=Platypus;CSQ=A|ENSG00000115596|ENST00000486233|Transcript|intron_variant&non_coding_transcript_variant|||||WNT6|processed_transcript|||||||,A|ENSG00000115596|ENST00000233948|Transcript|intron_variant|||||WNT6|protein_coding|YES||||||;GR=0.897;PH=0.178;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-20.07,0,-37.57:1:99:38:14 1/0:-39.44,0,-53.44:1:99:64:27 2 221198106 . T C 2663 PASS Source=Platypus;CSQ=C|ENSG00000239498|ENST00000432993|Transcript|intron_variant&non_coding_transcript_variant|||||AC114765.1|lincRNA|YES||||||;GR=0.118;PH=0.165;PS=0.051;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-184.4,-15.33,0:15:99:54:54 1/1:-162,-13.25,0:15:99:48:48 2 223642158 . AA - 2187 PASS Source=Platypus;CSQ=-||ENSR00001552171|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=0.576;PH=0.136;PS=0.008 GT:GL:GOF:GQ:NR:NV 1/1:-111.5,-9.33,0:17:93:31:31 1/1:-226.3,-18.94,0:19:99:64:64 2 224863802 . G A 2903 PASS Source=Platypus;CSQ=A|ENSG00000135919|ENST00000432738|Transcript|intron_variant|||||SERPINE2|protein_coding|||||||,A|ENSG00000135919|ENST00000423446|Transcript|downstream_gene_variant||||2689|SERPINE2|protein_coding|||||||,A|ENSG00000135919|ENST00000409304|Transcript|intron_variant|||||SERPINE2|protein_coding|||||||,A|ENSG00000135919|ENST00000489065|Transcript|downstream_gene_variant||||2467|SERPINE2|retained_intron|||||||,A|ENSG00000135919|ENST00000454956|Transcript|downstream_gene_variant||||2556|SERPINE2|protein_coding|||||||,A|ENSG00000135919|ENST00000409840|Transcript|intron_variant|||||SERPINE2|protein_coding|||||||,A|ENSG00000135919|ENST00000447280|Transcript|intron_variant|||||SERPINE2|protein_coding|YES||||||,A|ENSG00000135919|ENST00000258405|Transcript|intron_variant|||||SERPINE2|protein_coding|||||||,A||ENSR00001552331|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-4.78;PH=-1.205;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-11.62,-137.3:4:99:40:0 1/0:-77.75,0,-76.55:2:99:54:27 2 225106789 . T C 878 PASS Source=Platypus;CSQ=C|ENSG00000211987|ENST00000390698|Transcript|upstream_gene_variant||||2516|AC104802.1|miRNA|YES||||||;GR=-0.835;PH=-0.649;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-4.81,0,-77.51:10:48:39:9 0/0:0,-0.92,-91.2:18:10:45:8 2 226341873 . A G 2792 PASS Source=Platypus;CSQ=G|ENSG00000144460|ENST00000409269|Transcript|intron_variant|||||NYAP2|protein_coding|||||||,G|ENSG00000144460|ENST00000272907|Transcript|intron_variant|||||NYAP2|protein_coding|YES||||||;GR=1.2;PH=0.35;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-16.26,-211.9:2:99:55:0 1/0:-97.25,0,-64.05:0:99:50:24 2 233620779 . GC - 75 PASS Source=Platypus;CSQ=-|ENSG00000204120|ENST00000423659|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000424038|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GIGYF2|nonsense_mediated_decay|||||||,-|ENSG00000204120|ENST00000373563|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000421433|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000409196|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000409480|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000241409|ENST00000427571|Transcript|downstream_gene_variant||||4076|AC064852.4|3prime_overlapping_ncrna|YES||||||,-|ENSG00000204120|ENST00000425040|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000440945|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000463554|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||GIGYF2|processed_transcript|||||||,-|ENSG00000204120|ENST00000409451|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|YES||||||,-|ENSG00000204120|ENST00000430720|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000429187|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000428883|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000409547|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000456491|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||,-|ENSG00000204120|ENST00000373566|Transcript|intron_variant&feature_truncation|||||GIGYF2|protein_coding|||||||;GR=-0.968;PH=-0.194;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-113.44,0,-65.14:5:99:61:37 1/1:-181.6,-14.45,0:3:99:49:49 2 234411172 . G A 2458 PASS Source=Platypus;CSQ=A|ENSG00000085982|ENST00000251722|Transcript|intron_variant|||||USP40|protein_coding|||||||,A|ENSG00000085982|ENST00000409945|Transcript|intron_variant|||||USP40|protein_coding|||||||,A|ENSG00000085982|ENST00000427112|Transcript|intron_variant|||||USP40|protein_coding|||||||,A|ENSG00000085982|ENST00000450966|Transcript|intron_variant|||||USP40|protein_coding|YES||||||,A|ENSG00000085982|ENST00000483216|Transcript|intron_variant&non_coding_transcript_variant|||||USP40|retained_intron|||||||,A|ENSG00000085982|ENST00000430158|Transcript|intron_variant|||||USP40|protein_coding|||||||;GR=-1.13;PH=-1.015;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-21.58,0,-121.68:7:99:38:9 1/0:-18.13,0,-154.33:6:99:49:10 2 235295550 . CCT - 826 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.551;PH=-0.354;PS=0.014;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-17.76,-300:1:99:67:0 1/0:-181.45,0,-90.65:15:99:54:26 20 2520929 . C T 916 PASS Source=Platypus;CSQ=T|ENSG00000149488|ENST00000358864|Transcript|intron_variant|||||TMC2|protein_coding|YES||||||;GR=0.14;PH=0.182;PS=0.005;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-110.13,0,-101.33:2:99:74:37 0/0:0,-13.55,-169.4:2:99:48:0 20 5764642 . AC - 1914 PASS Source=Platypus;CSQ=-|ENSG00000171984|ENST00000442185|Transcript|intron_variant&feature_truncation|||||C20orf196|protein_coding|||||||,-|ENSG00000171984|ENST00000303142|Transcript|intron_variant&feature_truncation|||||C20orf196|protein_coding|YES||||||,-|ENSG00000171984|ENST00000445603|Transcript|intron_variant&feature_truncation|||||C20orf196|protein_coding|||||||;GR=0.235;PH=0.263;PS=0.071;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-124.53,0,-80.83:3:99:71:42 1/0:-56.66,0,-80.36:0:99:44:19 20 5910102 . C T 2512 PASS Source=Platypus;CSQ=T|ENSG00000215589|ENST00000400619|Transcript|upstream_gene_variant||||138|RP5-967N21.2|processed_pseudogene|YES||||||,T|ENSG00000089199|ENST00000378961|Transcript|downstream_gene_variant||||4095|CHGB|protein_coding|YES||||||;GR=0.364;PH=0.406;PS=0.12;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-148.2,-12.32,0:3:99:43:43 1/1:-147.3,-12.04,0:1:99:43:43 20 5911621 . ACTG - 123 PASS Source=Platypus;CSQ=-|ENSG00000215589|ENST00000400619|Transcript|upstream_gene_variant||||1657|RP5-967N21.2|processed_pseudogene|YES||||||;GR=-2.7;PH=-0.685;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-97.45,0,-116.25:1:99:75:35 0/1:-80.14,0,-98.24:5:99:58:26 20 6970443 . CA - 1818 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.23;PH=0.988;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-77.76,0,-38.56:5:99:42:28 0/0:0,-11.14,-133.3:2:99:39:0 20 7490390 . CA - 2757 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.256;PH=0.08;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-154.5,-12.64,0:35:99:45:45 1/1:-164.3,-12.94,0:41:99:45:45 20 8388269 . C T 2509 PASS Source=Platypus;CSQ=T|ENSG00000182621|ENST00000378641|Transcript|intron_variant|||||PLCB1|protein_coding|||||||,T|ENSG00000182621|ENST00000338037|Transcript|intron_variant|||||PLCB1|protein_coding|YES||||||,T|ENSG00000182621|ENST00000404098|Transcript|intron_variant|||||PLCB1|protein_coding|||||||,T|ENSG00000182621|ENST00000378637|Transcript|intron_variant|||||PLCB1|protein_coding|||||||;GR=-0.516;PH=-0.261;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-173.8,-14.75,0:12:99:51:51 1/1:-186.5,-15.35,0:2:99:53:53 20 11051316 . TAAC - 2430 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-5.01;PH=-1.415;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.55,-150.5:3:99:46:0 1/1:-177.7,-14.75,0:2:99:51:51 20 11971118 . GCAG - 1978 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.41;PH=-0.268;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-81.9,-4.52,0:3:45:34:16 0/1:-55.28,0,-47.48:1:99:42:12 20 12173245 rs542669032 G A 449 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;PH=-1.505;PS=0.024;REPMASK=SINE;1000G=0.000599042 GT:GL:GOF:GQ:NR:NV 0/1:-60.92,0,-39.72:3:99:33:13 0/1:-37.54,0,-40.04:16:99:22:11 20 14786507 . CA - 123 PASS Source=Platypus;CSQ=-|ENSG00000172264|ENST00000464883|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MACROD2|processed_transcript|||||||,-|ENSG00000172264|ENST00000497992|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MACROD2|processed_transcript|||||||,-|ENSG00000172264|ENST00000463861|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MACROD2|processed_transcript|||||||,-|ENSG00000172264|ENST00000217246|Transcript|intron_variant&feature_truncation|||||MACROD2|protein_coding|YES||||||,-|ENSG00000172264|ENST00000310348|Transcript|intron_variant&feature_truncation|||||MACROD2|protein_coding|||||||;GR=3.08;PH=2.04;PS=0.007 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.34,-142.4:5:99:45:0 0/1:-37.15,0,-78.55:3:99:49:17 20 15784664 . G A 1658 PASS Source=Platypus;CSQ=A|ENSG00000172264|ENST00000217246|Transcript|intron_variant|||||MACROD2|protein_coding|YES||||||,A|ENSG00000172264|ENST00000402914|Transcript|intron_variant|||||MACROD2|protein_coding|||||||,A|ENSG00000172264|ENST00000310348|Transcript|intron_variant|||||MACROD2|protein_coding|||||||;GR=-0.981;PH=-0.344;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-67.41,0,-93.21:7:99:62:28 0/0:0,-16.26,-190.3:4:99:56:0 20 16125848 . C T 2715 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-2.25;PH=-0.36;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-5.21,-36.1:4:52:37:0 0/1:-4.64,0,-20.64:11:46:33:9 20 16322735 . T C 1913 PASS Source=Platypus;CSQ=C|ENSG00000089177|ENST00000378003|Transcript|intron_variant|||||KIF16B|protein_coding|||||||,C|ENSG00000089177|ENST00000354981|Transcript|intron_variant|||||KIF16B|protein_coding|||||||,C|ENSG00000089177|ENST00000355755|Transcript|intron_variant|||||KIF16B|protein_coding|||||||;GR=-3.89;PH=-0.92;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.47,-193.4:3:99:57:0 0/1:-75.05,0,-87.55:1:99:56:26 20 19595703 . G A 2520 PASS Source=Platypus;CSQ=A|ENSG00000185052|ENST00000328041|Transcript|intron_variant|||||SLC24A3|protein_coding|YES||||||;GR=1.4;PH=0.402;PS=0.139 GT:GL:GOF:GQ:NR:NV 0/1:-16.27,0,-233.87:7:99:26:2 0/1:-29.3,0,-227.4:19:99:26:3 20 21305877 . T C 602 PASS Source=Platypus;CSQ=C|ENSG00000088930|ENST00000539513|Transcript|intron_variant|||||XRN2|protein_coding|||||||,C|ENSG00000088930|ENST00000430571|Transcript|intron_variant|||||XRN2|protein_coding|||||||,C|ENSG00000088930|ENST00000377191|Transcript|intron_variant|||||XRN2|protein_coding|YES||||||,C||ENSR00000233783|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.95;PH=1.593;PS=0.003 GT:GL:GOF:GQ:NR:NV 2/3:-1,-1,-1:17:62:15,12,15:3,4,1 1/3:-1,-1,-1:50:38:18,16,18:3,7,7 20 24399879 . G A 2943 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-5.21;PH=-1.793;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-219.4,-18.66,0:15:99:63:63 1/0:-79.35,0,-80.65:6:99:54:26 20 24675821 . CTGT - 2568 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.216;PH=-0.034;PS=0.005 GT:GL:GOF:GQ:NR:NV 1/1:-140,-12.32,0:31:99:49:45 1/1:-128.3,-10.96,0:24:99:42:41 20 24785888 . G A 2673 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.562;PH=0.21;PS=0.006 GT:GL:GOF:GQ:NR:NV 1/0:-37.92,0,-300:1:99:296:35 0/0:0,-55.97,-300:1:99:191:0 20 30989403 . G A 430 PASS Source=Platypus;CSQ=A|ENSG00000171456|ENST00000375687|Transcript|intron_variant|||||ASXL1|protein_coding|YES||||||,A|ENSG00000171456|ENST00000306058|Transcript|intron_variant|||||ASXL1|protein_coding|||||||,A|ENSG00000171456|ENST00000542461|Transcript|intron_variant|||||ASXL1|protein_coding|||||||,A|ENSG00000171456|ENST00000470145|Transcript|intron_variant&non_coding_transcript_variant|||||ASXL1|processed_transcript|||||||;GR=0.177;PH=0.284;PS=0.015;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-124.3,-32.51,0:5:99:43:40 1/1:-133,-36.38,0:7:99:45:42 20 32762115 . G A 371 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.998;PH=-0.435;PS=0.075;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-178.7:3:99:54:0 1/0:-69.71,0,-59.61:1:99:46:24 20 33709277 . GC - 219 alleleBias Source=Platypus;CSQ=-|ENSG00000088298|ENST00000540582|Transcript|intron_variant&feature_truncation|||||EDEM2|protein_coding|||||||,-|ENSG00000088298|ENST00000374491|Transcript|intron_variant&feature_truncation|||||EDEM2|protein_coding|||||||,-|ENSG00000088298|ENST00000374492|Transcript|intron_variant&feature_truncation|||||EDEM2|protein_coding|YES||||||,-|ENSG00000088298|ENST00000541621|Transcript|intron_variant&feature_truncation|||||EDEM2|protein_coding|||||||,-|ENSG00000201151|ENST00000364281|Transcript|upstream_gene_variant||||4267|SNORD56|snoRNA|YES||||||,-|ENSG00000088298|ENST00000542871|Transcript|intron_variant&feature_truncation|||||EDEM2|protein_coding|||||||,-||ENSR00000234255|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.122;PH=0.193;PS=0.161;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-242.7,-20.17,0:2:99:67:67 1/1:-155.9,-12.92,0:2:99:44:44 20 34761591 . T C 276 PASS Source=Platypus;CSQ=C|ENSG00000088367|ENST00000452261|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000338074|Transcript|intron_variant|||||EPB41L1|protein_coding|YES||||||,C|ENSG00000088367|ENST00000373950|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000406771|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000269650|ENST00000597622|Transcript|upstream_gene_variant||||3411|AL121895.1|protein_coding|YES||||||,C|ENSG00000088367|ENST00000373941|Transcript|upstream_gene_variant||||100|EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000427533|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000202028|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000432589|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000373945|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000430276|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000373946|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000447825|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C|ENSG00000088367|ENST00000441639|Transcript|intron_variant|||||EPB41L1|protein_coding|||||||,C||ENSR00000400425|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.06;PH=0.131;PS=0.65;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 1/0:-77.67,0,-81.47:1:99:56:27 1/0:-55.26,0,-46.86:2:99:35:18 20 35441977 . AA - 2517 PASS Source=Platypus;CSQ=-|ENSG00000149639|ENST00000237536|Transcript|intron_variant&feature_truncation|||||SOGA1|protein_coding|YES||||||,-|ENSG00000149639|ENST00000279034|Transcript|intron_variant&feature_truncation|||||SOGA1|protein_coding|||||||,-|ENSG00000149639|ENST00000465671|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SOGA1|nonsense_mediated_decay|||||||,-|ENSG00000149639|ENST00000357779|Transcript|intron_variant&feature_truncation|||||SOGA1|protein_coding|||||||,-|ENSG00000149639|ENST00000456801|Transcript|intron_variant&feature_truncation|||||SOGA1|protein_coding|||||||;GR=0.444;PH=0.393;PS=0.009;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-17.16,-200.6:4:99:61:0 1/0:-38.71,0,-69.01:2:99:40:15 20 35727243 rs151006747 G A 2120 PASS Source=Platypus;CSQ=A|ENSG00000101353|ENST00000343811|Transcript|downstream_gene_variant||||2386|MROH8|protein_coding|YES||||||,A|ENSG00000080839|ENST00000373664|Transcript|upstream_gene_variant||||2845|RBL1|protein_coding|YES||||||,A|ENSG00000101353|ENST00000400441|Transcript|downstream_gene_variant||||2395|MROH8|protein_coding|||||||,A|ENSG00000101353|ENST00000466091|Transcript|downstream_gene_variant||||2390|MROH8|processed_transcript|||||||,A|ENSG00000101353|ENST00000217333|Transcript|downstream_gene_variant||||2395|MROH8|protein_coding|||||||,A|ENSG00000101353|ENST00000441008|Transcript|downstream_gene_variant||||2387|MROH8|protein_coding|||||||,A|ENSG00000080839|ENST00000527999|Transcript|upstream_gene_variant||||2845|RBL1|nonsense_mediated_decay|||||||,A|ENSG00000101353|ENST00000417458|Transcript|downstream_gene_variant||||2386|MROH8|protein_coding|||||||,A|ENSG00000080839|ENST00000344359|Transcript|upstream_gene_variant||||2851|RBL1|protein_coding|||||||,A|ENSG00000269846|ENST00000598590|Transcript|downstream_gene_variant||||1662|RBL1|protein_coding|YES||||||;GR=0.649;PH=0.261;PS=0.012;1000G=0.000399361 GT:GL:GOF:GQ:NR:NV 0/1:-89.55,0,-59.25:2:99:52:31 0/1:-42.96,0,-76.56:2:99:41:16 20 36501964 . A G 1384 PASS Source=Platypus;CSQ=G|ENSG00000132792|ENST00000405275|Transcript|downstream_gene_variant||||1445|CTNNBL1|protein_coding|||||||,G|ENSG00000132792|ENST00000472237|Transcript|downstream_gene_variant||||1433|CTNNBL1|processed_transcript|||||||,G|ENSG00000132792|ENST00000373469|Transcript|downstream_gene_variant||||1433|CTNNBL1|protein_coding|||||||,G|ENSG00000132792|ENST00000473857|Transcript|downstream_gene_variant||||1433|CTNNBL1|processed_transcript|||||||,G|ENSG00000132792|ENST00000361383|Transcript|downstream_gene_variant||||1433|CTNNBL1|protein_coding|YES||||||,G|ENSG00000132792|ENST00000481674|Transcript|downstream_gene_variant||||1433|CTNNBL1|processed_transcript|||||||,G|ENSG00000132792|ENST00000373473|Transcript|downstream_gene_variant||||1433|CTNNBL1|protein_coding|||||||;GR=0.225;PH=0.257;PS=0.204;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-89.27,0,-78.87:1:99:56:30 0/0:0,-21.98,-270.2:2:99:74:0 20 37239953 . G A 1294 PASS Source=Platypus;CSQ=A|ENSG00000213959|ENST00000397037|Transcript|downstream_gene_variant||||3603|RP5-1100H13.3|processed_pseudogene|YES||||||,A|ENSG00000124143|ENST00000373345|Transcript|intron_variant|||||ARHGAP40|protein_coding|YES||||||;GR=0.149;PH=0.192;PS=0.113;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-139.7,-11.41,0:3:99:41:41 1/1:-145.4,-12.04,0:4:99:41:41 20 41866242 . C T 2121 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.99;PH=0.685;PS=0.116 GT:GL:GOF:GQ:NR:NV 0/1:-79.3,0,-78:12:99:57:28 0/0:0,-11.74,-147.7:7:99:41:0 20 42500718 . C T 608 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.118;PH=0.191;PS=0.174;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-4.76,-162.3:86:48:48:23 0/1:-6.05,0,-125.35:98:60:35:15 20 42847368 . T C 2312 PASS Source=Platypus;CSQ=C|ENSG00000223891|ENST00000439943|Transcript|intron_variant&non_coding_transcript_variant|||||OSER1-AS1|lincRNA|||||||,C|ENSG00000223891|ENST00000442383|Transcript|intron_variant&non_coding_transcript_variant|||||OSER1-AS1|lincRNA|||||||,C|ENSG00000223891|ENST00000437730|Transcript|intron_variant&non_coding_transcript_variant|||||OSER1-AS1|lincRNA|YES||||||,C|ENSG00000223891|ENST00000435163|Transcript|intron_variant&non_coding_transcript_variant|||||OSER1-AS1|lincRNA|||||||;GR=-0.931;PH=-0.151;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/1:-1,-1,-1:186:99:37,39:32,0 1/2:-1,-1,-1:214:99:37,35:18,0 20 43094398 . A G 273 PASS Source=Platypus;CSQ=G|ENSG00000168746|ENST00000372910|Transcript|upstream_gene_variant||||414|C20orf62|protein_coding|YES||||||,G|ENSG00000226243|ENST00000412502|Transcript|downstream_gene_variant||||806|RPL37AP1|processed_pseudogene|YES||||||,G|ENSG00000168746|ENST00000306731|Transcript|upstream_gene_variant||||430|C20orf62|protein_coding|||||||;GR=-1.14;PH=-0.601;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.82,-188.8:4:99:58:1 0/1:-42.12,0,-82.52:7:99:49:19 20 45491153 . A G 912 PASS Source=Platypus;CSQ=G|ENSG00000222874|ENST00000410942|Transcript|downstream_gene_variant||||2842|RN7SKP33|misc_RNA|YES||||||,G|ENSG00000235922|ENST00000423396|Transcript|downstream_gene_variant||||1049|RP11-323C15.1|processed_pseudogene|YES||||||;GR=-1.04;PH=-0.528;PS=0.004;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.94,-158.5:2:99:45:0 0/1:-67.82,0,-77.52:1:99:50:24 20 45547065 . AGC - 158 PASS Source=Platypus;CSQ=-|ENSG00000064655|ENST00000497062|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||EYA2|nonsense_mediated_decay|||||||,-|ENSG00000064655|ENST00000327619|Transcript|intron_variant&feature_truncation|||||EYA2|protein_coding|YES||||||,-|ENSG00000064655|ENST00000357410|Transcript|intron_variant&feature_truncation|||||EYA2|protein_coding|||||||;GR=0.421;PH=0.383;PS=0.007;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-1,-1,-1:14:1:40,51:7,14 0/2:-1,-1,-1:4:9:38,40:8,10 20 45653179 . G A 1923 PASS Source=Platypus;CSQ=A|ENSG00000064655|ENST00000497062|Transcript|intron_variant&NMD_transcript_variant|||||EYA2|nonsense_mediated_decay|||||||,A|ENSG00000064655|ENST00000317304|Transcript|intron_variant|||||EYA2|protein_coding|||||||,A|ENSG00000064655|ENST00000327619|Transcript|intron_variant|||||EYA2|protein_coding|YES||||||,A|ENSG00000064655|ENST00000458636|Transcript|intron_variant|||||EYA2|protein_coding|||||||,A|ENSG00000064655|ENST00000357410|Transcript|intron_variant|||||EYA2|protein_coding|||||||,A||ENSR00001022167|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.4;PH=0.564;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-66.5,-4.28,0:5:43:28:27 1/1:-114.68,-26.12,0:8:99:39:38 20 47492908 . AT - 1077 PASS Source=Platypus;CSQ=-||ENSR00000402245|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=3.38;PH=1.777;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/0:-42.63,0,-78.23:16:99:52:20 1/0:-62.36,0,-54.16:14:99:42:21 20 47705083 . G A 1183 PASS Source=Platypus;CSQ=A|ENSG00000124207|ENST00000542325|Transcript|intron_variant|||||CSE1L|protein_coding|||||||,A|ENSG00000124207|ENST00000396192|Transcript|intron_variant|||||CSE1L|protein_coding|||||||,A|ENSG00000124207|ENST00000469700|Transcript|upstream_gene_variant||||2217|CSE1L|processed_transcript|||||||,A|ENSG00000124207|ENST00000262982|Transcript|intron_variant|||||CSE1L|protein_coding|YES||||||;GR=-0.449;PH=-0.07;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-221.2,-18.66,0:15:99:64:64 0/1:-76.19,0,-104.19:7:99:58:25 20 48257215 . G A 2889 PASS Source=Platypus;CSQ=A|ENSG00000158470|ENST00000371711|Transcript|intron_variant|||||B4GALT5|protein_coding|YES||||||;GR=-2.26;PH=-0.224;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-38.53,0,-14.1:15:99:41:25 0/1:-0.49,0,-120.42:22:6:45:7 20 52099806 . A G 2821 PASS Source=Platypus;CSQ=G|ENSG00000182463|ENST00000603338|Transcript|intron_variant|||||TSHZ2|protein_coding|||||||,G|ENSG00000182463|ENST00000371497|Transcript|intron_variant|||||TSHZ2|protein_coding|YES||||||,G|ENSG00000259723|ENST00000558738|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-823G15.5|antisense|YES||||||,G|ENSG00000271774|ENST00000606932|Transcript|intron_variant&non_coding_transcript_variant|||||RP4-678D15.1|antisense|YES||||||,G|ENSG00000182463|ENST00000605656|Transcript|intron_variant&NMD_transcript_variant|||||TSHZ2|nonsense_mediated_decay|||||||;GR=0.0465;PH=0.115;PS=0.039;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-87.32,0,-37.22:1:99:45:29 1/0:-61.58,0,-49.68:4:99:40:21 20 53220796 . TT - 2228 PASS Source=Platypus;CSQ=-|ENSG00000101134|ENST00000395939|Transcript|intron_variant&feature_truncation|||||DOK5|protein_coding|||||||,-|ENSG00000101134|ENST00000262593|Transcript|intron_variant&feature_truncation|||||DOK5|protein_coding|YES||||||;GR=-0.599;PH=-0.22;PS=0.032 GT:GL:GOF:GQ:NR:NV 1/1:-229.9,-19.24,0:4:99:68:68 1/1:-223.8,-18.36,0:2:99:64:64 20 54298167 . C T 2882 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=2.47;PH=1.148;PS=0.991 GT:GL:GOF:GQ:NR:NV 0/1:-53.54,0,-57.54:20:99:41:20 0/0:0,-14.13,-171.2:1:99:51:0 20 54893742 . A G 1711 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.109;PH=0.156;PS=0.204;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-3.95,-74.4:58:39:29:2 0/1:-16.46,0,-104.66:125:99:42:7 20 57955536 . G A 2807 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-0.726;PH=-0.201;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.81,-169.5:2:99:47:0 1/0:-114.15,0,-29.85:0:99:49:36 20 58860206 . AAAT - 810 PASS Source=Platypus;CSQ=-|ENSG00000228340|ENST00000458422|Transcript|downstream_gene_variant||||535|RP5-1043L13.1|lincRNA|||||||,-|ENSG00000228340|ENST00000437035|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP5-1043L13.1|lincRNA|||||||,-|ENSG00000228340|ENST00000432910|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP5-1043L13.1|lincRNA|YES||||||,-|ENSG00000228340|ENST00000421257|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP5-1043L13.1|lincRNA|||||||;GR=0.217;PH=0.25;PS=0.105 GT:GL:GOF:GQ:NR:NV 1/0:-43.57,0,-56.07:6:99:33:15 1/1:-104.1,-8.43,0:3:84:29:29 20 62529381 . TA - 2154 PASS Source=Platypus;CSQ=-|ENSG00000101152|ENST00000470551|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||DNAJC5|nonsense_mediated_decay|||||||,-|ENSG00000101152|ENST00000369911|Transcript|intron_variant&feature_truncation|||||DNAJC5|protein_coding|||||||,-|ENSG00000101152|ENST00000360864|Transcript|intron_variant&feature_truncation|||||DNAJC5|protein_coding|YES||||||;GR=-0.256;PH=-0.088;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-72.55,0,-68.45:6:99:52:26 1/0:-73.07,0,-88.77:11:99:55:25 21 9496596 . CA - 203 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.119;PS=0.076;REPMASK=LINE;SD=0.994587 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.66,-231.2:2:99:63:0 0/1:-121.33,0,-94.63:5:99:70:38 21 9711085 . C T 2281 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.064;PS=0.165;REPMASK=LINE;SD=0.99681 GT:GL:GOF:GQ:NR:NV 1/1:-181.3,-15.3,0:1:99:53:53 1/1:-145.2,-12.03,0:0:99:42:42 21 10442645 . T C 430 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.173;PH=-0.821;PS=0.001;REPMASK=LINE;SD=0.981729 GT:GL:GOF:GQ:NR:NV 1/0:-300,0,-30.77:49:99:49:36 1/0:-300,0,-3.46:44:35:35:28 21 15859433 . T C 918 PASS Source=Platypus;CSQ=C|ENSG00000155307|ENST00000400566|Transcript|intron_variant|||||SAMSN1|protein_coding|||||||,C|ENSG00000155307|ENST00000400564|Transcript|intron_variant|||||SAMSN1|protein_coding|||||||,C|ENSG00000155307|ENST00000285670|Transcript|intron_variant|||||SAMSN1|protein_coding|YES||||||,C||ENSR00000315448|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.601;PH=0.103;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-158.01,0,-1.2:27:12:55:28 1/0:-30.91,0,-84.8:27:99:40:10 21 15961591 . T C 1276 PASS Source=Platypus;CSQ=C|ENSG00000223662|ENST00000449214|Transcript|intron_variant&non_coding_transcript_variant|||||SAMSN1-AS1|antisense|YES||||||,C|ENSG00000243440|ENST00000400562|Transcript|downstream_gene_variant||||4450|AF165138.7|protein_coding|YES||||||,C|ENSG00000243440|ENST00000435732|Transcript|downstream_gene_variant||||2660|AF165138.7|protein_coding|||||||;GR=-2.68;PH=-0.636;PS=0.912;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-199.7,-15.28,0:29:99:60:58 1/1:-154.7,-12.34,0:28:99:42:42 21 17020200 . AAA - 962 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.995;PH=0.707;PS=0.004;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-1.74,0,-54.04:10:18:24:3 1/0:-27.48,0,-82.68:10:99:38:9 21 18304616 . T C 2336 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.252;PH=0.06;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-294.7,-23.78,0:33:99:80:80 0/0:0,-15.63,-196.3:0:99:53:0 21 19938862 . C T 1010 PASS Source=Platypus;CSQ=T|ENSG00000224141|ENST00000437492|Transcript|intron_variant&non_coding_transcript_variant|||||AL109763.2|lincRNA|YES||||||,T|ENSG00000224141|ENST00000355189|Transcript|intron_variant&non_coding_transcript_variant|||||AL109763.2|lincRNA|||||||;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-89.51,0,-54.21:25:99:51:31 1/1:-217.2,-17.46,0:33:99:58:58 21 21451562 rs77094798 T C 128 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-1.02;PH=-1.645;PS=0.001;REPMASK=DNA;UK10K=286/7562;WGS500=28;1000G=0.0648962 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.33,-187.7:2:99:53:0 1/0:-75.75,0,-88.45:3:99:55:25 21 21781130 . C T 1242 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.47;PH=-1.808;PS=0.315;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-185.3,-15.05,0:19:99:54:54 1/0:-118.64,0,-70.14:13:99:62:37 21 22481193 . A G 1500 PASS Source=Platypus;CSQ=G|ENSG00000154654|ENST00000400546|Transcript|intron_variant|||||NCAM2|protein_coding|YES||||||,G|ENSG00000154654|ENST00000284894|Transcript|intron_variant|||||NCAM2|protein_coding|||||||;GR=-1.33;PH=-0.72;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-150.62,0,-0.56:4:7:58:26 0/1:-153.18,0,-1.34:4:14:56:32 21 23319696 . CTT - 780 PASS Source=Platypus;CSQ=-|ENSG00000227075|ENST00000452500|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000472.3|lincRNA|YES||||||;PH=0.107;PS=0.226;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.01,-138.2:5:99:49:0 1/0:-51.36,0,-47.76:7:99:45:19 21 24154034 . C T 2820 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.119;PS=0.097;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-85.54,0,-81.94:1:99:56:29 0/0:0,-15.35,-190.9:1:99:52:0 21 24422829 . T C 218 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.782;PH=0.64;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-183.1:4:99:54:0 1/0:-45.36,0,-90.06:2:99:45:16 21 28028578 . AGAA - 1073 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.14;PH=0.157;PS=0.223;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/0:-120.85,0,-97.05:37:99:35:14 1/0:-72.73,0,-70.83:38:99:22:7 21 31065913 . T C 189 PASS Source=Platypus;CSQ=C|ENSG00000171189|ENST00000327783|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000389124|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000399914|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000535441|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000399907|Transcript|intron_variant|||||GRIK1|protein_coding|YES||||||,C|ENSG00000171189|ENST00000399913|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000399909|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000472429|Transcript|intron_variant&non_coding_transcript_variant|||||GRIK1|processed_transcript|||||||,C|ENSG00000171189|ENST00000309434|Transcript|intron_variant|||||GRIK1|protein_coding|||||||,C|ENSG00000171189|ENST00000389125|Transcript|intron_variant|||||GRIK1|protein_coding|||||||;GR=4.25;PH=1.041;PS=1 GT:GL:GOF:GQ:NR:NV 1/0:-9.43,0,-75.43:12:94:38:7 0/0:0,-2.13,-124.1:12:21:48:2 21 32128844 . CC - 2758 PASS Source=Platypus;CSQ=-|ENSG00000187005|ENST00000335093|Transcript|upstream_gene_variant||||1098|KRTAP21-1|protein_coding|YES||||||;GR=0.397;PH=0.08;PS=0.136 GT:GL:GOF:GQ:NR:NV 0/1:-115.89,0,-93.09:1:99:70:38 1/1:-284.8,-22.98,0:7:99:82:81 21 33112598 . C T 2910 PASS Source=Platypus;CSQ=T|ENSG00000273091|ENST00000610276|Transcript|downstream_gene_variant||||3878|AP000255.6|lincRNA|YES||||||;GR=-0.298;PH=-1.083;PS=0.063;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-94.29,0,-69.19:13:99:56:32 0/0:0,-17.16,-216.6:0:99:60:0 21 33123262 . A G 2816 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.53;PH=0.47;PS=0.015;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-64.63,0,-79.83:0:99:53:24 0/1:-76.36,0,-106.16:0:99:63:27 21 35302327 . TT - 172 PASS Source=Platypus;CSQ=-|ENSG00000237945|ENST00000601471|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000599421|Transcript|upstream_gene_variant||||1139|LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000597626|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000598119|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000596365|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000400353|Transcript|upstream_gene_variant||||1190|LINC00649|antisense|||||||,-|ENSG00000237945|ENST00000427447|Transcript|upstream_gene_variant||||1136|LINC00649|antisense|||||||;PH=0.056;PS=0.09;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-44.75,0,-58.75:9:99:55:24 0/1:-34.75,0,-61.45:6:99:48:18 21 35721710 . A G 1231 PASS Source=Platypus;CSQ=G|ENSG00000272657|ENST00000362077|Transcript|intron_variant&non_coding_transcript_variant|||||AP000320.7|processed_transcript|YES||||||;GR=1.17;PH=0.327;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-19.43,0,-129.23:5:99:44:7 0/1:-25.99,0,-112.69:10:99:40:8 21 36130216 . TT - 266 PASS Source=Platypus;CSQ=-|ENSG00000234380|ENST00000420877|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000330.8|antisense|YES||||||;GR=0.444;PH=0.393;PS=0.184;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-82.25,0,-58.45:4:99:52:29 0/0:0,-9.23,-107.9:4:92:37:0 21 37253650 . AA - 2192 PASS Source=Platypus;CSQ=-|ENSG00000159216|ENST00000475045|Transcript|intron_variant&feature_truncation|||||RUNX1|protein_coding|||||||;GR=0.235;PH=0.263;PS=0.013;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-103.29,0,-61.49:2:99:49:30 1/0:-51.61,0,-84.21:9:99:51:21 21 37487040 . G A 2824 PASS Source=Platypus;CSQ=A|ENSG00000230212|ENST00000535199|Transcript|intron_variant&non_coding_transcript_variant|||||AP000688.14|sense_intronic|YES||||||;GR=0.0499;PH=0.007;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-78.64,0,-45.54:3:99:48:30 0/1:-72.95,0,-63.45:4:99:46:24 21 37848062 . TT - 2957 PASS Source=Platypus;CSQ=-|ENSG00000159261|ENST00000342108|Transcript|intron_variant&feature_truncation|||||CLDN14|protein_coding|||||||,-|ENSG00000159261|ENST00000399136|Transcript|intron_variant&feature_truncation|||||CLDN14|protein_coding|||||||,-|ENSG00000233818|ENST00000428667|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000695.4|antisense|YES||||||,-|ENSG00000159261|ENST00000399135|Transcript|intron_variant&feature_truncation|||||CLDN14|protein_coding|||||||,-|ENSG00000159261|ENST00000399137|Transcript|intron_variant&feature_truncation|||||CLDN14|protein_coding|YES||||||,-|ENSG00000230479|ENST00000429588|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000695.6|antisense|YES||||||;GR=0.149;PH=0.166;PS=0.157;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 1/1:-213,-17.46,0:3:99:61:59 1/1:-196.1,-15.65,0:1:99:54:54 21 39846735 . ATT - 429 PASS Source=Platypus;CSQ=-|ENSG00000157554|ENST00000398897|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000481609|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ERG|processed_transcript|||||||,-|ENSG00000157554|ENST00000453032|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000398910|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000288319|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000442448|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000429727|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000398919|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000398905|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000417133|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|YES||||||,-|ENSG00000157554|ENST00000485493|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ERG|processed_transcript|||||||,-|ENSG00000157554|ENST00000468474|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ERG|retained_intron|||||||,-|ENSG00000157554|ENST00000398911|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||,-|ENSG00000157554|ENST00000398907|Transcript|intron_variant&feature_truncation|||||ERG|protein_coding|||||||;GR=-3.67;PH=-0.819;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-123.13,0,-87.03:2:99:73:41 0/0:0,-17.41,-211.5:5:99:60:0 21 41317997 . G A 362 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.33;PH=-0.472;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-111.9,-9.02,0:0:90:31:31 0/0:0,-12.57,-153.9:3:99:44:0 21 41525269 . C T 1664 PASS Source=Platypus;CSQ=T|ENSG00000171587|ENST00000404019|Transcript|intron_variant|||||DSCAM|protein_coding|||||||,T|ENSG00000171587|ENST00000400454|Transcript|intron_variant|||||DSCAM|protein_coding|YES||||||;GR=-1.08;PH=-0.224;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-88.11,0,-48.51:2:99:47:29 1/0:-113.04,0,-59.54:1:99:57:36 21 41880470 . A G 1024 PASS Source=Platypus;CSQ=G|ENSG00000207147|ENST00000384418|Transcript|upstream_gene_variant||||4601|SNORA51|snoRNA|YES||||||,G|ENSG00000171587|ENST00000400454|Transcript|intron_variant|||||DSCAM|protein_coding|YES||||||,G||ENSR00001567028|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-2.85;PH=-1.29;PS=0.005 GT:GL:GOF:GQ:NR:NV 1/0:-107.55,0,-56.45:15:99:55:33 1/0:-55.56,0,-79.76:8:99:44:19 21 42007934 . TGCA - 1545 PASS Source=Platypus;CSQ=-|ENSG00000171587|ENST00000400454|Transcript|intron_variant&feature_truncation|||||DSCAM|protein_coding|YES||||||;GR=-0.612;PH=-0.187;PS=0.039 GT:GL:GOF:GQ:NR:NV 1/1:-142.8,-12.85,0:25:99:59:57 1/1:-126.8,-10.84,0:23:99:48:48 21 42788483 . G A 977 PASS Source=Platypus;CSQ=A|ENSG00000157601|ENST00000413778|Transcript|upstream_gene_variant||||4773|MX1|protein_coding|||||||,A|ENSG00000157601|ENST00000398600|Transcript|upstream_gene_variant||||3959|MX1|protein_coding|YES||||||,A|ENSG00000157601|ENST00000468506|Transcript|upstream_gene_variant||||3810|MX1|retained_intron|||||||,A|ENSG00000157601|ENST00000490220|Transcript|upstream_gene_variant||||3748|MX1|processed_transcript|||||||;PH=0.119;PS=0.22;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-87.64,0,-82.34:1:99:62:31 0/1:-66.1,0,-78.7:1:99:48:23 21 42861631 . T C 1324 PASS Source=Platypus;CSQ=C|ENSG00000184012|ENST00000497881|Transcript|intron_variant&non_coding_transcript_variant|||||TMPRSS2|processed_transcript|||||||,C|ENSG00000184012|ENST00000454499|Transcript|intron_variant|||||TMPRSS2|protein_coding|||||||,C|ENSG00000184012|ENST00000463138|Transcript|intron_variant&non_coding_transcript_variant|||||TMPRSS2|processed_transcript|||||||,C|ENSG00000184012|ENST00000398585|Transcript|intron_variant|||||TMPRSS2|protein_coding|YES||||||,C|ENSG00000184012|ENST00000424093|Transcript|intron_variant|||||TMPRSS2|protein_coding|||||||,C|ENSG00000184012|ENST00000455813|Transcript|downstream_gene_variant||||4652|TMPRSS2|protein_coding|||||||,C|ENSG00000184012|ENST00000458356|Transcript|intron_variant|||||TMPRSS2|protein_coding|||||||,C|ENSG00000184012|ENST00000332149|Transcript|intron_variant|||||TMPRSS2|protein_coding|||||||;GR=-2.72;PH=-0.681;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-66.58,0,-53.18:5:99:42:23 0/1:-68.05,0,-62.45:0:99:47:24 21 44028071 . A G 876 PASS Source=Platypus;CSQ=G|ENSG00000225431|ENST00000419628|Transcript|intron_variant&non_coding_transcript_variant|||||AP001626.1|lincRNA|YES||||||;GR=0.14;PH=0.157;PS=0.095 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:7:99:43,43:22,16 1/1:-1,-1,-1:8:76:33,33:29,0 21 45622199 . T C 1317 PASS Source=Platypus;CSQ=C|ENSG00000232698|ENST00000423967|Transcript|downstream_gene_variant||||4209|AP001058.3|lincRNA|YES||||||,C|ENSG00000232124|ENST00000437557|Transcript|intron_variant&non_coding_transcript_variant|||||AP001057.1|antisense|YES||||||,C||ENSR00000614643|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.892;PH=0.645;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-81.77,0,-75.57:2:99:52:27 0/0:0,-14.75,-186.9:1:99:49:0 22 16522116 . C T 2172 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;REPMASK=Satellite;SD=0.996027 GT:GL:GOF:GQ:NR:NV 0/0:0,-14.45,-165.2:6:99:51:0 0/1:-59.85,0,-78.15:2:99:46:20 22 16646828 . T C 512 PASS Source=Platypus;CSQ=C|ENSG00000184624|ENST00000425869|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF72P|unprocessed_pseudogene|YES||||||;PH=0.103;PS=0.3;REPMASK=LINE;SD=0.996027 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.26,-137.1:15:99:49:0 0/1:-67.07,0,-73.67:5:99:52:24 22 17099078 . TT - 1941 PASS Source=Platypus;CSQ=-|ENSG00000100181|ENST00000383140|Transcript|upstream_gene_variant||||1426|TPTEP1|lincRNA|||||||,-|ENSG00000267338|ENST00000438850|Transcript|downstream_gene_variant||||1074|KB-7G2.9|lincRNA|YES||||||,-|ENSG00000100181|ENST00000426585|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TPTEP1|lincRNA|YES||||||,-|ENSG00000100181|ENST00000400593|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TPTEP1|lincRNA|||||||,-|ENSG00000100181|ENST00000592107|Transcript|downstream_gene_variant||||3077|TPTEP1|lincRNA|||||||,-|ENSG00000100181|ENST00000591299|Transcript|downstream_gene_variant||||3855|TPTEP1|lincRNA|||||||,-|ENSG00000100181|ENST00000558085|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||TPTEP1|lincRNA|||||||,-|ENSG00000100181|ENST00000592918|Transcript|downstream_gene_variant||||3077|TPTEP1|lincRNA|||||||,-|ENSG00000100181|ENST00000588548|Transcript|downstream_gene_variant||||3084|TPTEP1|lincRNA|||||||;GR=0.109;PH=0.156;PS=0.511;REPMASK=LINE;SD=0.975046 GT:GL:GOF:GQ:NR:NV 1/0:-50.26,0,-31:10:99:50:14 1/0:-58.09,0,-46.36:13:99:52:8 22 17419941 . GGTC - 2647 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.298;PH=-1.112;PS=0.028;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-14.15,-238.3:1:99:50:0 1/0:-103.74,0,-133.74:1:99:56:24 22 18654850 . G A 1846 PASS Source=Platypus;CSQ=A|ENSG00000184979|ENST00000215794|Transcript|intron_variant|||||USP18|protein_coding|YES||||||;GR=-1.27;PH=-1.047;PS=0;REPMASK=SINE;SD=0.980621 GT:GL:GOF:GQ:NR:NV 1/0:-42.27,0,-88.87:7:99:49:19 0/0:0,-15.35,-190:3:99:53:0 22 23828554 . AA - 2040 PASS Source=Platypus;CSQ=-|ENSG00000178248|ENST00000539460|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000345.1|lincRNA|||||||,-|ENSG00000178248|ENST00000320372|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AP000345.1|lincRNA|YES||||||;GR=0.543;PH=0.443;PS=0.021;SD=0.923013 GT:GL:GOF:GQ:NR:NV 1/0:-17.69,0,-30.59:27:99:14:5 1/1:-65.8,-3.87,0:28:39:17:14 22 25165385 . CT - 600 PASS Source=Platypus;CSQ=-|ENSG00000184571|ENST00000332271|Transcript|intron_variant&feature_truncation|||||PIWIL3|protein_coding|YES||||||,-|ENSG00000184571|ENST00000527701|Transcript|intron_variant&feature_truncation|||||PIWIL3|protein_coding|||||||,-|ENSG00000184571|ENST00000533313|Transcript|intron_variant&feature_truncation|||||PIWIL3|protein_coding|||||||,-|ENSG00000184571|ENST00000532537|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PIWIL3|processed_transcript|||||||;GR=0.149;PH=0.192;PS=0.011;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-222.5,-19.5,0:4:99:70:70 1/0:-97.44,0,-83.34:1:99:64:36 22 25337083 . CA - 1967 PASS Source=Platypus;CSQ=-|ENSG00000206069|ENST00000423535|Transcript|upstream_gene_variant||||1581|TMEM211|protein_coding|||||||,-|ENSG00000206069|ENST00000407886|Transcript|intron_variant&feature_truncation|||||TMEM211|protein_coding|YES||||||,-|ENSG00000206069|ENST00000382744|Transcript|upstream_gene_variant||||1769|TMEM211|protein_coding|||||||;GR=0.491;PH=0.565;PS=0.088;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-84.85,0,-63.95:3:99:51:28 1/1:-189,-15.65,0:3:99:53:53 22 25453675 . A G 1409 PASS Source=Platypus;CSQ=G|ENSG00000197077|ENST00000494730|Transcript|intron_variant&non_coding_transcript_variant|||||KIAA1671|retained_intron|||||||,G|ENSG00000197077|ENST00000406486|Transcript|intron_variant|||||KIAA1671|protein_coding|||||||,G|ENSG00000197077|ENST00000358431|Transcript|intron_variant|||||KIAA1671|protein_coding|YES||||||,G||ENSR00000616024|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.235;PH=0.263;PS=0.01;REPMASK=SINE;SD=0.998941 GT:GL:GOF:GQ:NR:NV 0/2:-1,-1,-1:37:57:55,53:29,15 1/2:-1,-1,-1:33:81:45,41:26,8 22 27383838 . T C 205 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.37;PH=0.36;PS=0.009;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-9.82,-117.7:1:98:36:1 1/0:-12.6,0,-107.9:0:99:35:5 22 28297980 . GT - 1390 PASS Source=Platypus;CSQ=-|ENSG00000180957|ENST00000477861|Transcript|upstream_gene_variant||||3919|PITPNB|retained_intron|||||||,-|ENSG00000180957|ENST00000335272|Transcript|intron_variant&feature_truncation|||||PITPNB|protein_coding|YES||||||,-|ENSG00000180957|ENST00000455418|Transcript|intron_variant&feature_truncation|||||PITPNB|protein_coding|||||||,-|ENSG00000180957|ENST00000460566|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PITPNB|retained_intron|||||||,-|ENSG00000180957|ENST00000436663|Transcript|intron_variant&feature_truncation|||||PITPNB|protein_coding|||||||,-|ENSG00000180957|ENST00000320996|Transcript|intron_variant&feature_truncation|||||PITPNB|protein_coding|||||||,-|ENSG00000180957|ENST00000415296|Transcript|intron_variant&feature_truncation|||||PITPNB|protein_coding|||||||;GR=-1.68;PH=-0.975;PS=0.016;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.04,-149.6:2:99:44:0 0/1:-54.18,0,-71.48:0:99:43:19 22 28905813 . A G 763 PASS Source=Platypus;CSQ=G|ENSG00000100154|ENST00000397906|Transcript|intron_variant|||||TTC28|protein_coding|YES||||||;PH=0.138;PS=0.038;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-104.43,0,-154.13:14:99:70:54 0/0:0,-17.76,-275.3:6:99:61:19 22 31791177 . CC - 2054 PASS Source=Platypus;CSQ=-|ENSG00000185721|ENST00000416465|Transcript|upstream_gene_variant||||4418|DRG1|nonsense_mediated_decay|||||||,-|ENSG00000185721|ENST00000331457|Transcript|upstream_gene_variant||||4331|DRG1|protein_coding|YES||||||,-|ENSG00000185721|ENST00000433341|Transcript|upstream_gene_variant||||4425|DRG1|processed_transcript|||||||,-|ENSG00000185721|ENST00000486584|Transcript|upstream_gene_variant||||4441|DRG1|processed_transcript|||||||;GR=-3.61;PH=-0.763;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-59.06,0,-58.76:6:99:39:20 1/0:-89.94,0,-79.34:8:99:55:29 22 32016770 . CA - 2378 PASS Source=Platypus;CSQ=-|ENSG00000198089|ENST00000474741|Transcript|downstream_gene_variant||||2236|SFI1|processed_transcript|||||||,-|ENSG00000241878|ENST00000397500|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|||||||,-|ENSG00000241878|ENST00000336566|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|||||||,-|ENSG00000241878|ENST00000435900|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|||||||,-|ENSG00000198089|ENST00000400289|Transcript|downstream_gene_variant||||2236|SFI1|protein_coding|||||||,-|ENSG00000241878|ENST00000473770|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PISD|retained_intron|||||||,-|ENSG00000198089|ENST00000414585|Transcript|downstream_gene_variant||||2237|SFI1|protein_coding|||||||,-|ENSG00000241878|ENST00000422020|Transcript|downstream_gene_variant||||269|PISD|protein_coding|||||||,-|ENSG00000198089|ENST00000443011|Transcript|downstream_gene_variant||||2338|SFI1|protein_coding|||||||,-|ENSG00000241878|ENST00000266095|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|||||||,-|ENSG00000241878|ENST00000439502|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|||||||,-|ENSG00000198089|ENST00000357852|Transcript|downstream_gene_variant||||2236|SFI1|retained_intron|||||||,-|ENSG00000198089|ENST00000400288|Transcript|downstream_gene_variant||||2198|SFI1|protein_coding|YES||||||,-|ENSG00000241878|ENST00000442379|Transcript|downstream_gene_variant||||1077|PISD|protein_coding|||||||,-|ENSG00000241878|ENST00000460723|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PISD|retained_intron|||||||,-|ENSG00000241878|ENST00000429683|Transcript|downstream_gene_variant||||2899|PISD|protein_coding|||||||,-|ENSG00000198089|ENST00000452250|Transcript|downstream_gene_variant||||2237|SFI1|nonsense_mediated_decay|||||||,-|ENSG00000198089|ENST00000476577|Transcript|downstream_gene_variant||||2236|SFI1|retained_intron|||||||,-|ENSG00000198089|ENST00000382162|Transcript|downstream_gene_variant||||2236|SFI1|retained_intron|||||||,-|ENSG00000198089|ENST00000432498|Transcript|downstream_gene_variant||||2233|SFI1|protein_coding|||||||,-|ENSG00000198089|ENST00000464333|Transcript|downstream_gene_variant||||2237|SFI1|retained_intron|||||||,-|ENSG00000241878|ENST00000382151|Transcript|intron_variant&feature_truncation|||||PISD|protein_coding|YES||||||,-|ENSG00000241878|ENST00000437808|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||PISD|nonsense_mediated_decay|||||||,-|ENSG00000241878|ENST00000478893|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PISD|processed_transcript|||||||,-|ENSG00000198089|ENST00000540643|Transcript|downstream_gene_variant||||2237|SFI1|protein_coding|||||||,-|ENSG00000241878|ENST00000431201|Transcript|downstream_gene_variant||||2899|PISD|protein_coding|||||||,-|ENSG00000241878|ENST00000491342|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PISD|processed_transcript|||||||,-|ENSG00000241878|ENST00000474017|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PISD|retained_intron|||||||,-|ENSG00000198089|ENST00000443326|Transcript|downstream_gene_variant||||2237|SFI1|protein_coding|||||||;GR=3.23;PH=2.117;PS=0.021 GT:GL:GOF:GQ:NR:NV 1/0:-87.84,0,-89.34:27:99:59:30 1/0:-96.33,0,-114.63:24:99:70:33 22 32658123 . AG - 1984 PASS Source=Platypus;CSQ=-|ENSG00000242082|ENST00000434942|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP1-90G24.10|antisense|YES||||||;GR=0.158;PH=0.175;PS=0.039;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-85.61,0,-91.51:26:99:63:32 0/0:0,-14.75,-180.9:2:99:50:0 22 33475005 . GGC - 1789 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.805;PH=-0.218;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-32.93,0,-61.83:2:99:71:20 0/0:0,-9.93,-64.6:0:99:39:0 22 35268650 . TACT - 806 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.7;PH=0.478;PS=0 GT:GL:GOF:GQ:NR:NV 2/0:-1,-1,-1:528:99:233,233:104,60 1/2:-1,-1,-1:496:99:145,145:82,33 22 35526490 . G A 1372 PASS Source=Platypus;CSQ=A|ENSG00000273068|ENST00000610215|Transcript|downstream_gene_variant||||3078|CTA-714B7.7|lincRNA|YES||||||,A|ENSG00000233080|ENST00000423311|Transcript|intron_variant&non_coding_transcript_variant|||||CTA-714B7.5|lincRNA|YES||||||;GR=-2.78;PH=-1.118;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-112.09,0,-124.04:8:99:26:12 0/0:0,-8.4,-299.4:9:84:22:1 22 35860213 . A G 1802 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.765;PH=0.158;PS=0.006 GT:GL:GOF:GQ:NR:NV 1/0:-72.06,0,-57.66:4:99:47:25 0/0:0,-11.97,-137.2:1:99:45:0 22 40374270 . CAC - 16 PASS Source=Platypus;CSQ=-|ENSG00000100351|ENST00000344138|Transcript|downstream_gene_variant||||4545|GRAP2|protein_coding|YES||||||;GR=0.376;PH=0.175;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-85.54,0,-86.84:0:99:59:29 0/1:-79.74,0,-101.24:0:99:61:27 22 41079195 . G A 877 PASS Source=Platypus;CSQ=A|ENSG00000128285|ENST00000381433|Transcript|downstream_gene_variant||||1108|MCHR1|protein_coding|||||||,A|ENSG00000128285|ENST00000498400|Transcript|downstream_gene_variant||||1108|MCHR1|processed_transcript|||||||,A|ENSG00000128285|ENST00000465662|Transcript|downstream_gene_variant||||1779|MCHR1|processed_transcript|||||||,A|ENSG00000128285|ENST00000249016|Transcript|downstream_gene_variant||||377|MCHR1|protein_coding|YES||||||,A||ENSR00000618636|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.45;PH=1.022;PS=0.037 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.94,-225.9:5:99:65:0 0/1:-67.03,0,-66.63:3:99:48:22 22 41104130 . C T 353 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.119;PS=0.039;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-21.35,-259.3:1:99:70:0 0/1:-58.36,0,-80.76:0:99:47:19 22 41380978 . AA - 1743 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.0465;PH=0.115;PS=0.005;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.42,-226.2:2:99:63:0 1/0:-54.76,0,-51.66:15:99:35:18 22 42822690 . G A 755 PASS Source=Platypus;CSQ=A|ENSG00000235568|ENST00000355469|Transcript|intron_variant&NMD_transcript_variant|||||NFAM1|nonsense_mediated_decay|||||||,A|ENSG00000235568|ENST00000329021|Transcript|intron_variant|||||NFAM1|protein_coding|YES||||||;GR=1.85;PH=1.334;PS=0.264 GT:GL:GOF:GQ:NR:NV 0/1:-4.01,0,-15.41:6:40:29:9 0/1:-5.23,0,-11.33:5:52:30:8 22 43040374 . ATG - 752 PASS Source=Platypus;CSQ=-|ENSG00000100243|ENST00000407623|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|||||||,-|ENSG00000100243|ENST00000396303|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|||||||,-|ENSG00000100243|ENST00000361740|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|YES||||||,-|ENSG00000100243|ENST00000352397|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|||||||,-|ENSG00000100243|ENST00000466276|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CYB5R3|retained_intron|||||||,-|ENSG00000100243|ENST00000402438|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|||||||,-|ENSG00000249222|ENST00000505920|Transcript|upstream_gene_variant||||3767|ATP5L2|protein_coding|YES||||||,-|ENSG00000100243|ENST00000438270|Transcript|intron_variant&feature_truncation|||||CYB5R3|protein_coding|||||||;GR=-2.89;PH=-0.849;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-59.36,0,-97.76:2:99:58:22 0/0:0,-42.61,-136.7:2:99:44:0 22 43513886 . A G 2431 PASS Source=Platypus;CSQ=G|ENSG00000100290|ENST00000216115|Transcript|intron_variant|||||BIK|protein_coding|YES||||||;GR=0.158;PH=0.175;PS=0.266;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-212.1:4:99:65:0 1/0:-56.75,0,-105.55:3:99:51:19 22 45581480 . A G 797 PASS Source=Platypus;CSQ=G|ENSG00000093000|ENST00000396096|Transcript|downstream_gene_variant||||769|NUP50|protein_coding|||||||,G|ENSG00000100364|ENST00000336156|Transcript|downstream_gene_variant||||4739|KIAA0930|protein_coding|||||||,G|ENSG00000093000|ENST00000469163|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|3482||||NUP50|retained_intron|||||||,G|ENSG00000093000|ENST00000407019|Transcript|downstream_gene_variant||||769|NUP50|protein_coding|||||||,G|ENSG00000093000|ENST00000422489|Transcript|downstream_gene_variant||||2084|NUP50|protein_coding|||||||,G|ENSG00000093000|ENST00000347635|Transcript|3_prime_UTR_variant|2817||||NUP50|protein_coding|YES||||||,G|ENSG00000093000|ENST00000493456|Transcript|downstream_gene_variant||||1095|NUP50|processed_transcript|||||||,G|ENSG00000093000|ENST00000425733|Transcript|downstream_gene_variant||||442|NUP50|protein_coding|||||||;GR=3.31;PH=1.745;PS=0.014;SD=0.964902 GT:GL:GOF:GQ:NR:NV 1/1:-173.4,-14.15,0:1:99:49:49 1/1:-182.1,-15.05,0:1:99:51:51 22 45848989 . T C 2810 PASS Source=Platypus;CSQ=C|ENSG00000232363|ENST00000454439|Transcript|upstream_gene_variant||||4365|RP1-102D24.5|antisense|YES||||||,C||ENSR00000619511|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.319;PH=-0.144;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-108.3,-8.73,0:19:87:30:30 1/1:-221.5,-18.36,0:21:99:61:61 22 46307565 . C T 1201 PASS Source=Platypus;CSQ=T||ENSR00000619616|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,T||||intergenic_variant|||||||||||||;GR=-2.17;PH=-0.865;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-82.75,0,-53.55:14:99:47:27 1/1:-147,-12.04,0:13:99:45:45 22 46371894 . C T 1355 PASS Source=Platypus;CSQ=T|ENSG00000188064|ENST00000428540|Transcript|upstream_gene_variant||||105|WNT7B|protein_coding|||||||,T|ENSG00000265610|ENST00000578136|Transcript|downstream_gene_variant||||864|CR536603.1|miRNA|YES||||||,T|ENSG00000188064|ENST00000410058|Transcript|intron_variant|||||WNT7B|protein_coding|||||||,T|ENSG00000188064|ENST00000409496|Transcript|upstream_gene_variant||||3299|WNT7B|protein_coding|||||||,T|ENSG00000188064|ENST00000339464|Transcript|intron_variant|||||WNT7B|protein_coding|YES||||||,T|ENSG00000188064|ENST00000410089|Transcript|5_prime_UTR_variant|9||||WNT7B|protein_coding|||||||,T||ENSR00000619645|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.5;PH=1.321;PS=0.416;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 1/1:-202.7,-16.86,0:21:99:58:58 1/1:-149.4,-12.04,0:10:99:43:43 22 46879417 . AA - 2237 PASS Source=Platypus;CSQ=-|ENSG00000075275|ENST00000262738|Transcript|intron_variant&feature_truncation|||||CELSR1|protein_coding|YES||||||,-|ENSG00000075275|ENST00000395964|Transcript|intron_variant&feature_truncation|||||CELSR1|protein_coding|||||||,-|ENSG00000230634|ENST00000447383|Transcript|upstream_gene_variant||||1760|RP5-996D20.3|processed_pseudogene|YES||||||,-|ENSG00000075275|ENST00000454637|Transcript|intron_variant&feature_truncation|||||CELSR1|protein_coding|||||||;GR=0.59;PH=0.118;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.49,-216.2:2:99:65:0 1/0:-78.35,0,-91.05:0:99:54:25 22 47460176 . G A 2588 PASS Source=Platypus;CSQ=A|ENSG00000054611|ENST00000406733|Transcript|intron_variant|||||TBC1D22A|protein_coding|||||||,A|ENSG00000054611|ENST00000441162|Transcript|intron_variant&NMD_transcript_variant|||||TBC1D22A|nonsense_mediated_decay|||||||,A|ENSG00000054611|ENST00000337137|Transcript|intron_variant|||||TBC1D22A|protein_coding|YES||||||,A|ENSG00000054611|ENST00000355704|Transcript|intron_variant|||||TBC1D22A|protein_coding|||||||,A|ENSG00000054611|ENST00000394449|Transcript|intron_variant&NMD_transcript_variant|||||TBC1D22A|nonsense_mediated_decay|||||||,A|ENSG00000054611|ENST00000407381|Transcript|intron_variant|||||TBC1D22A|protein_coding|||||||;GR=-3.8;PH=-0.461;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-72.48,0,-77.28:2:99:51:24 0/0:0,-13.15,-161.4:3:99:48:1 22 47659317 . A G 95 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-4.97;PH=-1.549;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-199.2,-16.82,0:2:99:57:57 1/1:-142.6,-11.44,0:2:99:39:39 22 49007274 . T C 1973 PASS Source=Platypus;CSQ=C|ENSG00000219438|ENST00000358295|Transcript|intron_variant|||||FAM19A5|protein_coding|||||||,C|ENSG00000219438|ENST00000473898|Transcript|intron_variant&non_coding_transcript_variant|||||FAM19A5|processed_transcript|||||||,C|ENSG00000219438|ENST00000402357|Transcript|intron_variant|||||FAM19A5|protein_coding|YES||||||,C|ENSG00000219438|ENST00000336769|Transcript|intron_variant|||||FAM19A5|protein_coding|||||||;GR=-2.68;PH=-0.618;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-147.9,-12.34,0:1:99:43:43 1/1:-162.4,-13.25,0:5:99:47:47 22 49433125 . G A 2306 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=1.13;PH=0.477;PS=0.017;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 1/1:-150.6,-13.2,0:19:99:47:47 1/1:-142.5,-11.99,0:21:99:42:42 22 49987909 . C T 461 PASS Source=Platypus;CSQ=T|ENSG00000188511|ENST00000416411|Transcript|intron_variant&NMD_transcript_variant|||||C22orf34|nonsense_mediated_decay|||||||,T|ENSG00000188511|ENST00000414287|Transcript|intron_variant&NMD_transcript_variant|||||C22orf34|nonsense_mediated_decay|||||||;GR=0.422;PH=0.453;PS=0.014 GT:GL:GOF:GQ:NR:NV 0/1:-67.99,0,-48.29:2:99:43:25 0/0:0,-12.56,-145.2:2:99:47:0 22 50096632 . G A 291 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.235;PH=0.308;PS=0.005;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-128.6,-11.14,0:2:99:41:41 1/1:-124.7,-10.54,0:4:99:38:38 22 50943106 . A G 2395 PASS Source=Platypus;CSQ=G|ENSG00000100258|ENST00000505981|Transcript|downstream_gene_variant||||1019|LMF2|processed_transcript|||||||,G|ENSG00000025770|ENST00000523045|Transcript|upstream_gene_variant||||3569|NCAPH2|protein_coding|||||||,G|ENSG00000100258|ENST00000216080|Transcript|synonymous_variant|1582|471|V||LMF2|protein_coding|||||||,G|ENSG00000025770|ENST00000395701|Transcript|upstream_gene_variant||||3567|NCAPH2|protein_coding|||||||,G|ENSG00000025770|ENST00000420993|Transcript|upstream_gene_variant||||3539|NCAPH2|protein_coding|||||||,G|ENSG00000025770|ENST00000299821|Transcript|upstream_gene_variant||||3583|NCAPH2|protein_coding|YES||||||,G|ENSG00000100258|ENST00000380796|Transcript|intron_variant|||||LMF2|protein_coding|||||||,G|ENSG00000100258|ENST00000507607|Transcript|downstream_gene_variant||||1719|LMF2|retained_intron|||||||,G|ENSG00000025770|ENST00000418794|Transcript|upstream_gene_variant||||3582|NCAPH2|nonsense_mediated_decay|||||||,G|ENSG00000025770|ENST00000395698|Transcript|upstream_gene_variant||||3566|NCAPH2|protein_coding|||||||,G|ENSG00000100258|ENST00000514938|Transcript|downstream_gene_variant||||157|LMF2|retained_intron|||||||,G|ENSG00000100258|ENST00000474879|Transcript|synonymous_variant|1504|496|V||LMF2|protein_coding|YES||||||,G|ENSG00000025770|ENST00000518394|Transcript|upstream_gene_variant||||3568|NCAPH2|nonsense_mediated_decay|||||||,G|ENSG00000100258|ENST00000504717|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|360||||LMF2|retained_intron|||||||;GR=-7.55;PH=-0.823;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-78.54,0,-99.14:45:99:62:29 1/1:-157,-13.49,0:78:99:49:47 3 257243 . T C 2934 SC;MQ Source=Platypus;CSQ=C|ENSG00000134121|ENST00000449294|Transcript|upstream_gene_variant||||1975|CHL1|protein_coding|||||||,C|ENSG00000134121|ENST00000397491|Transcript|intron_variant|||||CHL1|protein_coding|||||||,C|ENSG00000134121|ENST00000421198|Transcript|intron_variant|||||CHL1|protein_coding|||||||,C|ENSG00000134121|ENST00000427688|Transcript|intron_variant|||||CHL1|protein_coding|||||||,C|ENSG00000134121|ENST00000486881|Transcript|downstream_gene_variant||||1881|CHL1|processed_transcript|||||||,C|ENSG00000134121|ENST00000435603|Transcript|intron_variant|||||CHL1|protein_coding|||||||,C|ENSG00000134121|ENST00000453040|Transcript|intron_variant&NMD_transcript_variant|||||CHL1|nonsense_mediated_decay|||||||,C|ENSG00000134121|ENST00000256509|Transcript|intron_variant|||||CHL1|protein_coding|YES||||||,C|ENSG00000134121|ENST00000489224|Transcript|intron_variant&non_coding_transcript_variant|||||CHL1|processed_transcript|||||||,C|ENSG00000134121|ENST00000481167|Transcript|intron_variant&non_coding_transcript_variant|||||CHL1|processed_transcript|||||||;GR=0.565;PH=0.47;PS=0.052;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.2,-169:4:99:59:4 1/0:-26.46,0,-97.46:0:99:46:14 3 778720 . AA - 1426 PASS Source=Platypus;CSQ=-|ENSG00000224957|ENST00000420823|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AC090044.1|lincRNA|YES||||||,-|ENSG00000224957|ENST00000442809|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||AC090044.1|lincRNA|||||||;GR=0.27;PH=0.063;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.15,-174.4:2:99:52:0 1/0:-61.17,0,-100.37:3:99:54:22 3 1163698 . TCT - 2463 PASS Source=Platypus;CSQ=-|ENSG00000134115|ENST00000413210|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CNTN6|nonsense_mediated_decay|||||||,-|ENSG00000134115|ENST00000539053|Transcript|intron_variant&feature_truncation|||||CNTN6|protein_coding|||||||,-|ENSG00000134115|ENST00000446702|Transcript|intron_variant&feature_truncation|||||CNTN6|protein_coding|YES||||||,-|ENSG00000134115|ENST00000350110|Transcript|intron_variant&feature_truncation|||||CNTN6|protein_coding|||||||,-|ENSG00000134115|ENST00000394261|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CNTN6|nonsense_mediated_decay|||||||,-|ENSG00000134115|ENST00000397479|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CNTN6|nonsense_mediated_decay|||||||;GR=-1.85;PH=-0.697;PS=0.046;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-6.62,0,-138.72:10:66:46:6 0/0:0,-9.9,-115.4:17:99:43:14 3 2253463 . T C 563 PASS Source=Platypus;CSQ=C|ENSG00000144619|ENST00000455083|Transcript|intron_variant|||||CNTN4|protein_coding|||||||,C|ENSG00000144619|ENST00000427741|Transcript|intron_variant&NMD_transcript_variant|||||CNTN4|nonsense_mediated_decay|||||||,C|ENSG00000144619|ENST00000418658|Transcript|intron_variant|||||CNTN4|protein_coding|||||||,C|ENSG00000144619|ENST00000422330|Transcript|intron_variant|||||CNTN4|protein_coding|||||||;GR=1.61;PH=0.993;PS=0.013 GT:GL:GOF:GQ:NR:NV 1/0:-77.31,0,-46.51:11:99:49:28 1/0:-39.98,0,-57.98:9:99:43:19 3 7131300 . TTAT - 2803 PASS Source=Platypus;CSQ=-|ENSG00000196277|ENST00000402647|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000486284|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000448328|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000389335|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000443259|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000467425|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000389336|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000435689|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000357716|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|YES||||||,-|ENSG00000196277|ENST00000440923|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000403881|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||;GR=-5.34;PH=-1.008;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-52.63,0,-99.13:6:99:71:26 1/0:-43.49,0,-100.89:11:99:59:20 3 7322404 . CA - 1971 PASS Source=Platypus;CSQ=-|ENSG00000196277|ENST00000402647|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000486284|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000448328|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000389335|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000467425|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000389336|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||,-|ENSG00000196277|ENST00000357716|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|YES||||||,-|ENSG00000196277|ENST00000435689|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000440923|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||GRM7|nonsense_mediated_decay|||||||,-|ENSG00000196277|ENST00000403881|Transcript|intron_variant&feature_truncation|||||GRM7|protein_coding|||||||;GR=3.19;PH=1.305;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/1:-77.07,0,-80.07:3:99:56:27 0/1:-91.64,0,-85.34:3:99:60:31 3 11947059 . C T 2108 PASS Source=Platypus;CSQ=T|ENSG00000231897|ENST00000449657|Transcript|upstream_gene_variant||||942|MARK2P14|unprocessed_pseudogene|YES||||||,T|ENSG00000225275|ENST00000510577|Transcript|downstream_gene_variant||||4340|NUP210P2|unprocessed_pseudogene|YES||||||,T|ENSG00000251038|ENST00000511122|Transcript|downstream_gene_variant||||4049|AC090958.5|unprocessed_pseudogene|YES||||||;GR=0.412;PH=0.445;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-91.76,0,-126.26:2:99:72:31 0/0:0,-19.27,-238.9:0:99:66:0 3 13133893 . G A 2183 PASS Source=Platypus;CSQ=A||ENSR00001357826|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,A||||intergenic_variant|||||||||||||;GR=1.16;PH=0.372;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-91.45,0,-102.25:6:99:68:31 0/1:-74.65,0,-65.55:10:99:53:29 3 14512821 . TG - 1216 PASS Source=Platypus;CSQ=-|ENSG00000131389|ENST00000360861|Transcript|intron_variant&feature_truncation|||||SLC6A6|protein_coding|||||||,-|ENSG00000131389|ENST00000458124|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SLC6A6|nonsense_mediated_decay|||||||,-|ENSG00000131389|ENST00000427436|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SLC6A6|nonsense_mediated_decay|||||||,-|ENSG00000131389|ENST00000452151|Transcript|upstream_gene_variant||||928|SLC6A6|protein_coding|||||||,-|ENSG00000131389|ENST00000454876|Transcript|intron_variant&feature_truncation|||||SLC6A6|protein_coding|YES||||||;GR=-3.99;PH=-0.862;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-10.84,-236.1:4:99:35:0 1/0:-121.29,0,-63.59:5:99:31:18 3 16565838 . T C 2614 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-3.53;PH=-0.498;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:24:99:62,62:57,27 1/2:-1,-1,-1:21:99:53,53:47,19 3 30147423 . G A 186 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.225;PH=0.3;PS=0.009;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-78.06,0,-48.56:1:99:46:27 0/0:0,-15.95,-193.6:0:99:53:0 3 31927028 . CCTC - 2688 PASS Source=Platypus;CSQ=-|ENSG00000144645|ENST00000396556|Transcript|intron_variant&feature_truncation|||||OSBPL10|protein_coding|YES||||||,-|ENSG00000144645|ENST00000467955|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000452791|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000438237|Transcript|intron_variant&feature_truncation|||||OSBPL10|protein_coding|||||||,-|ENSG00000144645|ENST00000480671|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000465626|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|retained_intron|||||||,-|ENSG00000144645|ENST00000466604|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000485205|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000463504|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||,-|ENSG00000144645|ENST00000479173|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||OSBPL10|processed_transcript|||||||;GR=-0.492;PH=-0.148;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-90.5,0,-57.1:2:99:49:28 1/1:-157.9,-12.64,0:2:99:45:45 3 44223189 . T C 2847 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.241;PH=-0.085;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.26,-200.9:6:99:56:0 1/0:-67.21,0,-86.41:2:99:50:23 3 45693003 . T C 213 PASS Source=Platypus;CSQ=C|ENSG00000144791|ENST00000465039|Transcript|intron_variant&non_coding_transcript_variant|||||LIMD1|processed_transcript|||||||,C|ENSG00000144791|ENST00000273317|Transcript|intron_variant|||||LIMD1|protein_coding|YES||||||,C|ENSG00000144791|ENST00000440097|Transcript|intron_variant|||||LIMD1|protein_coding|||||||;GR=0.122;PH=0.166;PS=0.019;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-62.43,0,-80.73:5:99:56:24 0/1:-49.16,0,-67.46:4:99:42:17 3 48201158 . TTT - 321 PASS Source=Platypus;CSQ=-|ENSG00000235627|ENST00000456366|Transcript|upstream_gene_variant||||1506|SNRPFP4|processed_pseudogene|YES||||||,-|ENSG00000164045|ENST00000302506|Transcript|intron_variant&feature_truncation|||||CDC25A|protein_coding|YES||||||,-|ENSG00000164045|ENST00000459900|Transcript|downstream_gene_variant||||4732|CDC25A|processed_transcript|||||||,-|ENSG00000164045|ENST00000351231|Transcript|intron_variant&feature_truncation|||||CDC25A|protein_coding|||||||;GR=-0.0601;PH=-0.016;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.6,-185.9:0:99:55:0 0/1:-112.9,0,-73.9:1:99:55:33 3 61533488 . G A 1052 PASS Source=Platypus;CSQ=A||ENSR00001365735|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,A||||intergenic_variant|||||||||||||;GR=0.462;PH=0.482;PS=0.654;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-106.41,0,-42.31:2:99:58:37 0/1:-61.59,0,-60.39:6:99:43:20 3 62986530 . ATGT - 1543 PASS Source=Platypus;CSQ=-|ENSG00000244342|ENST00000468072|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00698|lincRNA|YES||||||,-|ENSG00000244342|ENST00000465262|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00698|lincRNA|||||||,-|ENSG00000244342|ENST00000465684|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00698|lincRNA|||||||,-|ENSG00000244342|ENST00000475886|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00698|lincRNA|||||||;PH=0.077;PS=0.121 GT:GL:GOF:GQ:NR:NV 1/1:-23.4,-0.11,0:25:4:8:7 ./.:-0.3,0,-0.3:10:3:0:0 3 63196657 . G A 777 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.91;PH=-0.79;PS=0 GT:GL:GOF:GQ:NR:NV 2/0:-1,-1,-1:5:99:27,27:1,12 1/0:-1,-1,-1:4:99:30,30:13,14 3 63545205 . T C 788 PASS Source=Platypus;CSQ=C|ENSG00000163630|ENST00000467934|Transcript|downstream_gene_variant||||2807|SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000496889|Transcript|downstream_gene_variant||||2880|SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000460711|Transcript|intron_variant|||||SYNPR|protein_coding|||||||,C|ENSG00000163630|ENST00000472899|Transcript|downstream_gene_variant||||2788|SYNPR|nonsense_mediated_decay|||||||,C|ENSG00000163630|ENST00000465156|Transcript|intron_variant|||||SYNPR|protein_coding|||||||,C|ENSG00000163630|ENST00000460142|Transcript|downstream_gene_variant||||2788|SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000493532|Transcript|intron_variant&non_coding_transcript_variant|||||SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000295894|Transcript|intron_variant|||||SYNPR|protein_coding|||||||,C|ENSG00000163630|ENST00000478456|Transcript|downstream_gene_variant||||2833|SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000478744|Transcript|intron_variant&non_coding_transcript_variant|||||SYNPR|processed_transcript|||||||,C|ENSG00000163630|ENST00000479198|Transcript|intron_variant|||||SYNPR|protein_coding|||||||,C|ENSG00000163630|ENST00000450542|Transcript|intron_variant&NMD_transcript_variant|||||SYNPR|nonsense_mediated_decay|||||||,C|ENSG00000163630|ENST00000468110|Transcript|intron_variant&NMD_transcript_variant|||||SYNPR|nonsense_mediated_decay|||||||,C|ENSG00000163630|ENST00000478300|Transcript|intron_variant|||||SYNPR|protein_coding|YES||||||,C|ENSG00000163630|ENST00000498449|Transcript|intron_variant&NMD_transcript_variant|||||SYNPR|nonsense_mediated_decay|||||||;GR=1.82;PH=0.534;PS=0.029 GT:GL:GOF:GQ:NR:NV 1/1:-193.5,-16.54,0:2:99:58:58 1/0:-89.25,0,-68.15:1:99:55:30 3 70970457 . C T 879 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.207;PH=0.293;PS=0.147;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-5.72,-137.4:1:57:22:0 1/1:-300,-17.76,0:9:99:55:52 3 75904999 . TT - 2408 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=3.04;PH=1.618;PS=0.007;SD=0.945637 GT:GL:GOF:GQ:NR:NV 1/1:-150.7,-12.32,0:2:99:43:43 0/1:-63.15,0,-72.35:2:99:45:21 3 76900271 . A G 2375 PASS Source=Platypus;CSQ=G|ENSG00000185008|ENST00000602589|Transcript|intron_variant|||||ROBO2|protein_coding|||||||,G|ENSG00000185008|ENST00000475034|Transcript|intron_variant&non_coding_transcript_variant|||||ROBO2|processed_transcript|||||||,G|ENSG00000185008|ENST00000487694|Transcript|intron_variant|||||ROBO2|protein_coding|YES||||||;GR=-1.13;PH=-0.2;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-113.84,0,-57.14:3:99:59:38 1/0:-58.65,0,-70.85:2:99:47:21 3 79778756 . T C 2211 PASS Source=Platypus;CSQ=C|ENSG00000169855|ENST00000464233|Transcript|intron_variant|||||ROBO1|protein_coding|YES||||||;GR=2;PH=0.318;PS=0.097;UK10K=1/7562 GT:GL:GOF:GQ:NR:NV 2/4:-1,-1,-1:10:99:31,31,31,30:22,22,22,22 1/3:-1,-1,-1:5:99:40,40,40,34:20,20,20,18 3 79945316 . A G 727 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=2.59;PH=0.226;PS=0.013 GT:GL:GOF:GQ:NR:NV 0/1:-54.6,0,-164.84:21:99:45:15 0/1:-38.75,0,-93.94:34:99:36:13 3 83792332 . TT - 1121 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.57;PH=0.794;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-50.57,0,-60.17:11:99:43:16 1/1:-123.88,-8.65,0:22:86:45:16 3 86189141 . GGG - 1718 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.207;PH=0.284;PS=0.014;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-68.32,0,-92.02:2:99:56:26 1/1:-189.8,-15.35,0:2:99:54:54 3 88470084 . TTT - 349 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.06;PH=0.212;PS=0;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 0/1:-79.35,0,-63.55:5:99:48:26 0/1:-57.75,0,-76.05:6:99:48:23 3 99040163 . T C 2791 PASS Source=Platypus;CSQ=C||ENSR00001369144|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=1.59;PH=0.468;PS=0.035;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-183,-16.49,0:4:99:57:57 1/0:-48.67,0,-92.47:2:99:52:19 3 100489180 . C T 2011 PASS Source=Platypus;CSQ=T|ENSG00000154175|ENST00000487012|Transcript|intron_variant&non_coding_transcript_variant|||||ABI3BP|retained_intron|||||||,T|ENSG00000154175|ENST00000497021|Transcript|upstream_gene_variant||||4430|ABI3BP|retained_intron|||||||,T|ENSG00000154175|ENST00000495591|Transcript|intron_variant|||||ABI3BP|protein_coding|||||||,T|ENSG00000154175|ENST00000497395|Transcript|downstream_gene_variant||||4955|ABI3BP|protein_coding|||||||,T|ENSG00000154175|ENST00000284322|Transcript|intron_variant|||||ABI3BP|protein_coding|YES||||||,T|ENSG00000154175|ENST00000383691|Transcript|intron_variant|||||ABI3BP|protein_coding|||||||,T|ENSG00000154175|ENST00000470336|Transcript|intron_variant&non_coding_transcript_variant|||||ABI3BP|retained_intron|||||||,T|ENSG00000154175|ENST00000469764|Transcript|downstream_gene_variant||||4268|ABI3BP|processed_transcript|||||||,T|ENSG00000154175|ENST00000471714|Transcript|intron_variant|||||ABI3BP|protein_coding|||||||,T|ENSG00000154175|ENST00000486770|Transcript|downstream_gene_variant||||551|ABI3BP|protein_coding|||||||;GR=-1.38;PH=-0.275;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-138.37,0,-57.37:5:99:67:45 0/0:0,-16.23,-199.3:1:99:55:0 3 101110449 . C T 2585 PASS Source=Platypus;CSQ=T|ENSG00000138468|ENST00000394091|Transcript|intron_variant|||||SENP7|protein_coding|||||||,T|ENSG00000138468|ENST00000314261|Transcript|intron_variant|||||SENP7|protein_coding|||||||,T|ENSG00000138468|ENST00000394095|Transcript|intron_variant|||||SENP7|protein_coding|YES||||||,T|ENSG00000138468|ENST00000348610|Transcript|intron_variant|||||SENP7|protein_coding|||||||,T|ENSG00000138468|ENST00000358203|Transcript|intron_variant|||||SENP7|protein_coding|||||||,T|ENSG00000138468|ENST00000394094|Transcript|intron_variant|||||SENP7|protein_coding|||||||,T||ENSR00001369566|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;PH=0.064;PS=0.313;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-247.1,-19.87,0:12:99:69:69 0/0:0,-11.44,-145:2:99:39:0 3 106326053 . CCC - 2770 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.461;PH=0.076;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-225.9,-18.66,0:1:99:63:63 1/1:-208.9,-17.11,0:2:99:59:59 3 112981693 . A G 2158 PASS Source=Platypus;CSQ=G|ENSG00000144857|ENST00000355385|Transcript|intron_variant|||||BOC|protein_coding|||||||,G|ENSG00000144857|ENST00000471963|Transcript|intron_variant&non_coding_transcript_variant|||||BOC|retained_intron|||||||,G|ENSG00000144857|ENST00000495514|Transcript|intron_variant|||||BOC|protein_coding|YES||||||,G|ENSG00000144857|ENST00000498710|Transcript|intron_variant|||||BOC|protein_coding|||||||,G|ENSG00000144857|ENST00000273395|Transcript|intron_variant|||||BOC|protein_coding|||||||,G|ENSG00000144857|ENST00000477178|Transcript|intron_variant&non_coding_transcript_variant|||||BOC|processed_transcript|||||||;GR=-1.82;PH=-0.29;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-139.85,0,-76.45:2:99:51:25 0/1:-65.66,0,-93.66:1:99:40:11 3 114354060 . C T 1618 PASS Source=Platypus;CSQ=T|ENSG00000181722|ENST00000491500|Transcript|intron_variant&non_coding_transcript_variant|||||ZBTB20|processed_transcript|||||||,T|ENSG00000181722|ENST00000492665|Transcript|intron_variant&non_coding_transcript_variant|||||ZBTB20|processed_transcript|||||||,T|ENSG00000181722|ENST00000479879|Transcript|intron_variant&non_coding_transcript_variant|||||ZBTB20|processed_transcript|||||||,T|ENSG00000181722|ENST00000480832|Transcript|intron_variant&non_coding_transcript_variant|||||ZBTB20|processed_transcript|||||||,T|ENSG00000181722|ENST00000462705|Transcript|intron_variant|||||ZBTB20|protein_coding|||||||,T|ENSG00000181722|ENST00000471418|Transcript|intron_variant|||||ZBTB20|protein_coding|||||||,T|ENSG00000181722|ENST00000463890|Transcript|intron_variant&non_coding_transcript_variant|||||ZBTB20|processed_transcript|||||||,T|ENSG00000181722|ENST00000357258|Transcript|intron_variant|||||ZBTB20|protein_coding|||||||,T|ENSG00000181722|ENST00000464560|Transcript|intron_variant|||||ZBTB20|protein_coding|||||||;GR=-0.535;PH=-0.164;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:4:99:40,40:23,23 2/2:-1,-1,-1:2:17:47,47:26,26 3 120414068 . A G 2442 PASS Source=Platypus;CSQ=G|ENSG00000144840|ENST00000273375|Transcript|intron_variant|||||RABL3|protein_coding|YES||||||,G|ENSG00000144840|ENST00000465022|Transcript|intron_variant&NMD_transcript_variant|||||RABL3|nonsense_mediated_decay|||||||,G|ENSG00000144840|ENST00000485161|Transcript|intron_variant&NMD_transcript_variant|||||RABL3|nonsense_mediated_decay|||||||,G|ENSG00000144840|ENST00000481015|Transcript|intron_variant&NMD_transcript_variant|||||RABL3|nonsense_mediated_decay|||||||,G|ENSG00000144840|ENST00000483733|Transcript|intron_variant|||||RABL3|protein_coding|||||||,G|ENSG00000144840|ENST00000468192|Transcript|intron_variant&non_coding_transcript_variant|||||RABL3|processed_transcript|||||||,G|ENSG00000144840|ENST00000473654|Transcript|intron_variant&NMD_transcript_variant|||||RABL3|nonsense_mediated_decay|||||||,G|ENSG00000144840|ENST00000491398|Transcript|intron_variant&non_coding_transcript_variant|||||RABL3|processed_transcript|||||||;GR=3.79;PH=2.238;PS=0.009 GT:GL:GOF:GQ:NR:NV 0/0:0,-8.72,-94.6:6:87:43:2 1/0:-17.63,0,-70.67:2:99:50:8 3 132640298 . T C 883 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.578;PH=0.154;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-31.97,0,-58.07:13:99:43:23 1/1:-110.8,-9.33,0:24:93:53:53 3 137801082 . C T 803 PASS Source=Platypus;CSQ=T|ENSG00000158163|ENST00000473850|Transcript|downstream_gene_variant||||4734|DZIP1L|retained_intron|||||||,T|ENSG00000158163|ENST00000466301|Transcript|upstream_gene_variant||||411|DZIP1L|retained_intron|||||||,T|ENSG00000158163|ENST00000469243|Transcript|intron_variant|||||DZIP1L|protein_coding|||||||,T|ENSG00000158163|ENST00000327532|Transcript|intron_variant|||||DZIP1L|protein_coding|YES||||||,T|ENSG00000158163|ENST00000488595|Transcript|intron_variant&non_coding_transcript_variant|||||DZIP1L|processed_transcript|||||||,T||ENSR00001374892|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.61;PH=0.412;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-17,-3.63,0:2:36:26:15 1/1:-16.7,-2.8,0:2:28:26:13 3 138826428 . A G 1213 PASS Source=Platypus;CSQ=G|ENSG00000175110|ENST00000495075|Transcript|intron_variant|||||MRPS22|protein_coding|YES||||||,G|ENSG00000175110|ENST00000495225|Transcript|upstream_gene_variant||||2818|MRPS22|protein_coding|||||||,G|ENSG00000232416|ENST00000418282|Transcript|intron_variant&non_coding_transcript_variant|||||BPESC1|lincRNA|YES||||||;GR=-0.874;PH=-0.203;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-100.13,0,-98.14:3:99:60:31 1/0:-97.62,0,-99.29:1:99:55:27 3 140152859 . CT - 701 PASS Source=Platypus;CSQ=-|ENSG00000158258|ENST00000458420|Transcript|intron_variant&feature_truncation|||||CLSTN2|protein_coding|YES||||||,-|ENSG00000158258|ENST00000511524|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CLSTN2|retained_intron|||||||,-||ENSR00001375211|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.49;PH=-0.376;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-10.54,-204.8:5:99:37:0 1/1:-177.8,-10.24,0:18:99:35:28 3 140259409 . A G 1889 PASS Source=Platypus;CSQ=G|ENSG00000158258|ENST00000458420|Transcript|intron_variant|||||CLSTN2|protein_coding|YES||||||,G|ENSG00000158258|ENST00000511524|Transcript|intron_variant&non_coding_transcript_variant|||||CLSTN2|retained_intron|||||||,G||ENSR00001375224|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-4.65;PH=-0.948;PS=0.823 GT:GL:GOF:GQ:NR:NV 0/1:-35.29,0,-200.89:3:99:83:18 0/1:-99.61,0,-119.61:3:99:77:35 3 148553288 . CAGA - 1825 PASS Source=Platypus;CSQ=-|ENSG00000153002|ENST00000494888|Transcript|downstream_gene_variant||||973|CPB1|protein_coding|||||||,-|ENSG00000153002|ENST00000468341|Transcript|intron_variant&feature_truncation|||||CPB1|protein_coding|||||||,-|ENSG00000153002|ENST00000282957|Transcript|intron_variant&feature_truncation|||||CPB1|protein_coding|||||||,-|ENSG00000153002|ENST00000491148|Transcript|intron_variant&feature_truncation|||||CPB1|protein_coding|YES||||||,-|ENSG00000153002|ENST00000465718|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CPB1|retained_intron|||||||,-|ENSG00000153002|ENST00000462345|Transcript|intron_variant&feature_truncation|||||CPB1|protein_coding|||||||,-|ENSG00000153002|ENST00000484877|Transcript|upstream_gene_variant||||2671|CPB1|processed_transcript|||||||;GR=1.45;PH=0.518;PS=0.025;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-63.78,0,-85.68:4:99:53:24 1/0:-62.56,0,-63.86:1:99:44:21 3 151479661 . T C 378 PASS Source=Platypus;CSQ=C|ENSG00000197953|ENST00000445270|Transcript|downstream_gene_variant||||534|AADACL2|nonsense_mediated_decay|||||||,C|ENSG00000242908|ENST00000475855|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-454C18.2|antisense|||||||,C|ENSG00000242097|ENST00000489539|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|139||||RP11-64D22.1|processed_pseudogene|YES||||||,C|ENSG00000242908|ENST00000483843|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-454C18.2|antisense|YES||||||,C|ENSG00000197953|ENST00000356517|Transcript|downstream_gene_variant||||4107|AADACL2|protein_coding|YES||||||;GR=0.362;PH=0.077;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-51.49,0,-71.39:5:99:52:22 1/1:-84.4,-6.85,0:5:68:34:29 3 152565539 . CT - 247 PASS Source=Platypus;CSQ=-||ENSR00001485090|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=0.235;PH=0.308;PS=0.693;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-16.8,-205.5:0:99:57:0 1/0:-103.75,0,-55.05:0:99:53:33 3 157483510 . T C 313 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-7.15;PH=-1.202;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-184.9,-16.5,0:3:99:59:59 1/0:-71.57,0,-70.47:3:99:53:25 3 158432154 . TG - 2935 PASS Source=Platypus;CSQ=-|ENSG00000118849|ENST00000479756|Transcript|intron_variant&feature_truncation|||||RARRES1|protein_coding|||||||,-|ENSG00000118849|ENST00000498640|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RARRES1|processed_transcript|||||||,-|ENSG00000118849|ENST00000237696|Transcript|intron_variant&feature_truncation|||||RARRES1|protein_coding|YES||||||,-|ENSG00000118849|ENST00000462663|Transcript|upstream_gene_variant||||3493|RARRES1|processed_transcript|||||||;GR=-4.85;PH=-1.326;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-58.49,0,-53.79:2:99:41:21 0/0:0,-13.85,-168.1:0:99:45:0 3 162751667 . G A 2484 PASS Source=Platypus;CSQ=A|ENSG00000241168|ENST00000490357|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-10O22.1|lincRNA|YES||||||;GR=0.217;PH=0.292;PS=0.205;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-179.9,-14.97,0:29:99:52:52 1/1:-169.7,-13.55,0:27:99:47:46 3 163937909 . A G 2672 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.007;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-18.04,-211.5:8:99:61:0 0/1:-88.86,0,-63.16:2:99:53:29 3 164679973 . A G 1120 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=2.47;PH=0.764;PS=0.03 GT:GL:GOF:GQ:NR:NV 1/1:-189.8,-15.95,0:2:99:55:55 1/0:-76.71,0,-74.61:7:99:51:25 3 172601654 . G A 2012 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.235;PH=0.308;PS=0.07;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-16.74,-194.6:3:99:59:0 1/0:-76.25,0,-71.25:2:99:53:27 3 190133185 . T C 1130 PASS Source=Platypus;CSQ=C|ENSG00000113946|ENST00000264734|Transcript|downstream_gene_variant||||3253|CLDN16|protein_coding|YES||||||;GR=0.69;PH=0.531;PS=0.007;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-102.45,0,-68.15:12:99:49:25 0/0:0,-11.74,-163.5:3:99:41:0 3 192827028 . GT - 1920 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.694;PH=-0.216;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-58.55,0,-89.85:1:99:50:20 0/0:0,-12.3,-151.5:2:99:42:0 4 2590928 . ATT - 644 PASS Source=Platypus;CSQ=-|ENSG00000063978|ENST00000508235|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||RNF4|nonsense_mediated_decay|||||||;GR=-4.13;PH=-1.086;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-223.8:6:99:65:0 0/1:-129.54,0,-70.54:0:99:65:40 4 4967895 . CA - 221 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.567;PH=0.164;PS=0.008 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.25,-163.4:3:99:46:0 0/1:-80.94,0,-100.54:4:99:62:29 4 8456964 . A G 2698 PASS Source=Platypus;CSQ=G|ENSG00000155275|ENST00000532477|Transcript|intron_variant&non_coding_transcript_variant|||||TRMT44|processed_transcript|||||||,G|ENSG00000251186|ENST00000515186|Transcript|upstream_gene_variant||||295|RP11-689P11.3|antisense|YES||||||,G|ENSG00000155275|ENST00000513449|Transcript|intron_variant|||||TRMT44|protein_coding|||||||,G|ENSG00000155275|ENST00000389737|Transcript|intron_variant|||||TRMT44|protein_coding|YES||||||;GR=-2;PH=-1.614;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-79.87,0,-90.67:4:99:63:29 1/1:-200.8,-16.78,0:4:99:58:58 4 12599169 . C T 387 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.207;PH=0.284;PS=0.074;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-202.6,-16.56,0:1:99:57:57 1/0:-78.25,0,-71.15:1:99:48:25 4 12794636 . G A 681 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-2.08;PH=-0.708;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-69.07,0,-75.77:4:99:54:24 0/0:0,-13.53,-159.9:1:99:48:0 4 20671420 . GT - 2988 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.064;PS=0.264;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-57.49,0,-97.09:2:99:61:26 1/1:-234.2,-20.17,0:1:99:69:68 4 26102733 . TG - 721 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.68;PH=-0.36;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-44.06,0,-44.56:1:99:50:18 1/1:-128.8,-12.64,0:2:99:52:41 4 27715577 . A G 272 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.32;PH=0.861;PS=0.002;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-77.25,0,-56.55:15:99:47:26 1/1:-210,-17.43,0:25:99:62:62 4 28835465 . C T 1612 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-2.32;PH=-0.749;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-167.7,-13.55,0:19:99:48:48 1/0:-51.59,0,-65.59:9:99:42:18 4 35461449 . CAGG - 105 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.149;PH=0.192;PS=0.443;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-100.65,0,-58.05:3:99:52:32 1/0:-88.64,0,-88.94:2:99:58:29 4 35503989 . T C 2781 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.587;PH=-0.23;PS=0.031;REPMASK=Low_complexity GT:GL:GOF:GQ:NR:NV 1/1:-221.4,-18.03,0:1:99:62:62 1/0:-68.66,0,-60.76:2:99:42:21 4 37937004 . C T 81 PASS Source=Platypus;CSQ=T|ENSG00000065882|ENST00000402522|Transcript|intron_variant|||||TBC1D1|protein_coding|||||||,T|ENSG00000065882|ENST00000261439|Transcript|intron_variant|||||TBC1D1|protein_coding|YES||||||,T|ENSG00000065882|ENST00000510573|Transcript|intron_variant&NMD_transcript_variant|||||TBC1D1|nonsense_mediated_decay|||||||,T|ENSG00000065882|ENST00000508802|Transcript|intron_variant|||||TBC1D1|protein_coding|||||||;GR=-1.84;PH=-0.538;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-85.13,0,-96.13:2:99:62:29 0/0:0,-13.55,-167.4:1:99:48:0 4 39250292 . T C 368 PASS Source=Platypus;CSQ=C|ENSG00000157796|ENST00000288634|Transcript|intron_variant|||||WDR19|protein_coding|||||||,C|ENSG00000157796|ENST00000512095|Transcript|intron_variant&non_coding_transcript_variant|||||WDR19|retained_intron|||||||,C|ENSG00000157796|ENST00000399820|Transcript|intron_variant|||||WDR19|protein_coding|YES||||||,C|ENSG00000157796|ENST00000506869|Transcript|intron_variant&NMD_transcript_variant|||||WDR19|nonsense_mediated_decay|||||||;PH=0.103;PS=0.094;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-159.34,-0.99,0:12:10:37:23 0/0:0,-9.03,-180.6:5:90:42:2 4 44475403 . C T 1686 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-1.41;PH=-0.45;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-75.15,0,-66.85:4:99:53:29 1/0:-58.22,0,-60.42:3:99:40:21 4 46227144 . CTC - 1912 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.149;PH=0.192;PS=0.07;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-105.84,0,-59.54:5:99:56:34 1/0:-75.65,0,-74.85:4:99:50:25 4 53984111 . AAA - 1447 PASS Source=Platypus;CSQ=-|ENSG00000184178|ENST00000388940|Transcript|intron_variant&feature_truncation|||||SCFD2|protein_coding|||||||,-|ENSG00000184178|ENST00000401642|Transcript|intron_variant&feature_truncation|||||SCFD2|protein_coding|YES||||||;GR=2.97;PH=1.598;PS=0.053 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.86,-262.5:1:99:58:0 1/0:-97.94,0,-123.34:0:99:56:22 4 57397162 . A G 2351 PASS Source=Platypus;CSQ=G|ENSG00000249693|ENST00000512175|Transcript|missense_variant|388|107|H/R||THEGL|protein_coding|YES|tolerated(0.98)|benign(0)||||,G||ENSR00001431445|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.7;PH=-0.534;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-192.9,-16.26,0:5:99:59:59 1/1:-181.5,-15.62,0:5:99:55:55 4 60613874 . A G 1908 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;PH=0.103;PS=0.039;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/2:-1,-1,-1:8:99:48,48:11,11 0/1:-1,-1,-1:17:99:41,41:19,19 4 62782160 . CTG - 1258 PASS Source=Platypus;CSQ=-|ENSG00000150471|ENST00000507625|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000508946|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506700|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000502815|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000509896|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000511324|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000545650|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506720|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000504896|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514591|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|YES||||||,-|ENSG00000150471|ENST00000508693|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506746|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514996|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000512091|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514157|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000507164|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||;GR=0.648;PH=0.598;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-1,-1,-1:3:99:52,52:51,0 1/2:-1,-1,-1:2:99:41,41:41,16 4 62896598 . TC - 1645 PASS Source=Platypus;CSQ=-|ENSG00000150471|ENST00000507625|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000508946|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506700|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000502815|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000509896|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000511324|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000545650|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506720|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000504896|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514591|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|YES||||||,-|ENSG00000150471|ENST00000508693|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000506746|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514996|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000512091|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000514157|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||,-|ENSG00000150471|ENST00000507164|Transcript|intron_variant&feature_truncation|||||LPHN3|protein_coding|||||||;GR=3.23;PH=0.791;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-159.2,-12.64,0:4:99:44:44 1/1:-188.4,-15.35,0:11:99:53:53 4 65644059 . TCT - 574 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.251;PH=-0.079;PS=0.016;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-12.9,-153.6:2:99:47:0 0/1:-56.31,0,-58.01:3:99:43:21 4 66614155 . C T 1334 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.276;PH=0.039;PS=0.004 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.66,-223:3:99:63:0 1/0:-75.45,0,-69.85:0:99:48:25 4 70445270 . A G 2496 PASS Source=Platypus;CSQ=G|ENSG00000251177|ENST00000506662|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-401E5.2|unprocessed_pseudogene|YES||||||;GR=-1.18;PH=-0.663;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-76.95,0,-120.65:4:99:52:19 0/1:-112.74,0,-98.54:3:99:55:24 4 77976473 . G A 1063 PASS Source=Platypus;CSQ=A|ENSG00000118816|ENST00000507788|Transcript|downstream_gene_variant||||3239|CCNI|protein_coding|||||||,A|ENSG00000118816|ENST00000505609|Transcript|downstream_gene_variant||||724|CCNI|protein_coding|||||||,A|ENSG00000118816|ENST00000511943|Transcript|downstream_gene_variant||||3|CCNI|nonsense_mediated_decay|||||||,A|ENSG00000118816|ENST00000537948|Transcript|missense_variant|924|160|P/S||CCNI|protein_coding||deleterious(0.02)|benign(0.231)||||,A|ENSG00000118816|ENST00000237654|Transcript|missense_variant|1097|174|P/S||CCNI|protein_coding|YES|deleterious(0.03)|benign(0.341)||||,A|ENSG00000118816|ENST00000513774|Transcript|downstream_gene_variant||||3190|CCNI|protein_coding|||||||,A|ENSG00000118816|ENST00000504697|Transcript|downstream_gene_variant||||745|CCNI|processed_transcript|||||||,A|ENSG00000118816|ENST00000515468|Transcript|intron_variant|||||CCNI|protein_coding|||||||,A|ENSG00000118816|ENST00000506614|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|439||||CCNI|retained_intron|||||||;GR=5.86;PH=2.937;PS=1 GT:GL:GOF:GQ:NR:NV 1/0:-43.89,0,-45.19:24:99:35:15 0/0:0,-8.7,-103.9:9:87:37:0 4 78171227 . AA - 2188 PASS Source=Platypus;CSQ=-|ENSG00000138764|ENST00000514756|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNG2|processed_transcript|||||||,-|ENSG00000138764|ENST00000497512|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CCNG2|processed_transcript|||||||;GR=-1.06;PH=-1.375;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-75.68,0,-75.28:9:99:59:30 0/0:0,-12.64,-152.8:7:99:43:0 4 79605072 . C T 356 PASS Source=Platypus;CSQ=T|ENSG00000251442|ENST00000504675|Transcript|downstream_gene_variant||||1526|LINC01094|lincRNA|||||||,T|ENSG00000251442|ENST00000503539|Transcript|downstream_gene_variant||||1255|LINC01094|lincRNA|YES||||||,T|ENSG00000251442|ENST00000507802|Transcript|downstream_gene_variant||||3023|LINC01094|lincRNA|||||||,T|ENSG00000251442|ENST00000512322|Transcript|downstream_gene_variant||||1219|LINC01094|lincRNA|||||||;GR=-1.44;PH=-0.438;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-58.22,0,-73.52:2:99:43:18 0/1:-80.35,0,-83.55:1:99:53:26 4 82325381 . T C 173 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=2.92;PH=1.598;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/1:-56.4,0,-53.8:11:99:40:20 0/0:0,-16.43,-188.5:1:99:59:0 4 96448989 . C T 1325 PASS Source=Platypus;CSQ=T|ENSG00000182168|ENST00000506749|Transcript|intron_variant|||||UNC5C|protein_coding|||||||,T|ENSG00000182168|ENST00000513796|Transcript|intron_variant|||||UNC5C|protein_coding|||||||,T|ENSG00000182168|ENST00000453304|Transcript|intron_variant|||||UNC5C|protein_coding|YES||||||,T|ENSG00000182168|ENST00000504962|Transcript|intron_variant|||||UNC5C|protein_coding|||||||;GR=-3.54;PH=-0.58;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-1.94,0,-12.64:3:19:37:3 0/1:-2.08,0,-9.28:6:21:33:1 4 99816703 . T C 576 PASS Source=Platypus;CSQ=C|ENSG00000151247|ENST00000515638|Transcript|intron_variant&NMD_transcript_variant|||||EIF4E|nonsense_mediated_decay|||||||,C|ENSG00000151247|ENST00000504432|Transcript|intron_variant|||||EIF4E|protein_coding|||||||,C|ENSG00000151247|ENST00000450253|Transcript|intron_variant|||||EIF4E|protein_coding|||||||,C|ENSG00000151247|ENST00000505194|Transcript|upstream_gene_variant||||4654|EIF4E|processed_transcript|||||||,C|ENSG00000151247|ENST00000511644|Transcript|intron_variant|||||EIF4E|protein_coding|||||||,C|ENSG00000151247|ENST00000280892|Transcript|intron_variant|||||EIF4E|protein_coding|||||||,C|ENSG00000151247|ENST00000507665|Transcript|intron_variant&non_coding_transcript_variant|||||EIF4E|retained_intron|||||||,C|ENSG00000151247|ENST00000504472|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|158||||EIF4E|processed_transcript|||||||,C|ENSG00000151247|ENST00000505829|Transcript|upstream_gene_variant||||3981|EIF4E|retained_intron|||||||,C|ENSG00000151247|ENST00000505992|Transcript|intron_variant|||||EIF4E|protein_coding|YES||||||;GR=-1.94;PH=-0.874;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-74.94,0,-99.74:15:99:59:27 0/0:0,-12.94,-159.1:18:99:44:0 4 104340048 . TG - 2196 PASS Source=Platypus;CSQ=-|ENSG00000248740|ENST00000513793|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-328K4.1|lincRNA|||||||,-|ENSG00000248740|ENST00000508099|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-328K4.1|lincRNA|YES||||||;GR=0.823;PH=0.188;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-58.96,0,-65.16:7:99:44:20 0/0:0,-13.8,-166.5:1:99:48:0 4 105259052 . A G 1854 PASS Source=Platypus;CSQ=G|ENSG00000251170|ENST00000514327|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-729M20.1|lincRNA|YES||||||,G|ENSG00000251170|ENST00000505680|Transcript|downstream_gene_variant||||1862|RP11-729M20.1|lincRNA|||||||;GR=0.171;PH=0.237;PS=0.229;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-189.8,-15.35,0:37:99:51:51 1/1:-232.8,-19.57,0:36:99:66:65 4 105941557 . T C 2849 PASS Source=Platypus;CSQ=C|ENSG00000248373|ENST00000506148|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-556I14.1|lincRNA|||||||,C|ENSG00000248373|ENST00000506386|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-556I14.1|lincRNA|YES||||||;GR=0.109;PH=0.156;PS=0.17;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.52,-161.7:15:99:52:0 1/0:-68.81,0,-63.01:0:99:44:23 4 106534427 rs75619397 G A 493 PASS Source=Platypus;CSQ=A|ENSG00000236699|ENST00000506828|Transcript|intron_variant&non_coding_transcript_variant|||||ARHGEF38|processed_transcript|||||||,A|ENSG00000236699|ENST00000265154|Transcript|intron_variant|||||ARHGEF38|protein_coding|||||||,A|ENSG00000236699|ENST00000420470|Transcript|intron_variant|||||ARHGEF38|protein_coding|YES||||||;GR=3.12;PH=1.053;PS=0.004;1000G=0.0103834 GT:GL:GOF:GQ:NR:NV 1/0:-65.49,0,-9.89:25:99:40:12 0/0:0,-5.97,-25:38:60:34:21 4 108530077 . T C 813 PASS Source=Platypus;CSQ=C|ENSG00000138801|ENST00000514815|Transcript|intron_variant&non_coding_transcript_variant|||||PAPSS1|processed_transcript|||||||,C|ENSG00000138801|ENST00000265174|Transcript|downstream_gene_variant||||4745|PAPSS1|protein_coding|YES||||||;GR=-7.53;PH=-1.403;PS=0 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:2:15:32,32:4,4 1/2:-1,-1,-1:2:8:32,32:7,7 4 120097824 . G A 2350 PASS Source=Platypus;CSQ=A|ENSG00000172399|ENST00000307128|Transcript|intron_variant|||||MYOZ2|protein_coding|YES||||||;GR=0.369;PH=0.008;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-9.26,0,-23.82:5:93:45:14 0/0:0,-7.98,-25.75:4:80:32:1 4 120867101 . GGG - 2700 PASS Source=Platypus;CSQ=-|ENSG00000250183|ENST00000505862|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-96A1.4|transcribed_unprocessed_pseudogene|YES||||||,-|ENSG00000250392|ENST00000505122|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-700N1.1|lincRNA|YES||||||,-|ENSG00000200553|ENST00000363683|Transcript|upstream_gene_variant||||1183|Y_RNA|misc_RNA|YES||||||;GR=-0.741;PH=-0.266;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-17.77,0,-9.87:5:99:37:13 0/0:0,-4.8,-23.4:8:48:30:2 4 123179347 . A G 375 PASS Source=Platypus;CSQ=G|ENSG00000138688|ENST00000455637|Transcript|intron_variant|||||KIAA1109|protein_coding|||||||,G|ENSG00000138688|ENST00000446180|Transcript|intron_variant|||||KIAA1109|protein_coding|||||||,G|ENSG00000138688|ENST00000264501|Transcript|intron_variant|||||KIAA1109|protein_coding|YES||||||,G|ENSG00000138688|ENST00000388738|Transcript|intron_variant|||||KIAA1109|protein_coding|||||||,G|ENSG00000138688|ENST00000419325|Transcript|intron_variant|||||KIAA1109|protein_coding|||||||;GR=0.3;PH=-0.224;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-31.5,-2.41,0:3:24:11:7 1/0:-6.1,0,-2.8:10:28:5:2 4 126687269 . C T 1091 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=2.2;PH=0.857;PS=0.359 GT:GL:GOF:GQ:NR:NV 1/1:-157.4,-13.19,0:2:99:45:45 1/1:-181.6,-14.68,0:4:99:51:51 4 129722587 . G A 2342 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.13;PH=-0.343;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.94,-151:5:99:49:0 1/0:-65.53,0,-56.53:1:99:42:21 4 134413219 . CAT - 476 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.064;PS=0.226;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-67.17,0,-63.67:14:99:48:23 1/1:-167.1,-14.42,0:25:99:48:48 4 139435943 . T C 1464 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-2.12;PH=-0.698;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-199.8,-16.54,0:18:99:56:56 1/1:-180.8,-14.45,0:21:99:49:49 4 143236563 . T C 2040 PASS Source=Platypus;CSQ=C|ENSG00000109452|ENST00000508116|Transcript|intron_variant|||||INPP4B|protein_coding|||||||,C|ENSG00000109452|ENST00000509777|Transcript|intron_variant|||||INPP4B|protein_coding|||||||,C|ENSG00000250835|ENST00000502948|Transcript|upstream_gene_variant||||1828|LSM3P4|processed_pseudogene|YES||||||,C|ENSG00000109452|ENST00000512630|Transcript|intron_variant&NMD_transcript_variant|||||INPP4B|nonsense_mediated_decay|||||||,C|ENSG00000109452|ENST00000506297|Transcript|intron_variant&NMD_transcript_variant|||||INPP4B|nonsense_mediated_decay|||||||,C|ENSG00000109452|ENST00000262992|Transcript|intron_variant|||||INPP4B|protein_coding|||||||,C|ENSG00000109452|ENST00000513000|Transcript|intron_variant|||||INPP4B|protein_coding|YES||||||,C|ENSG00000109452|ENST00000308502|Transcript|intron_variant|||||INPP4B|protein_coding|||||||,C|ENSG00000109452|ENST00000510812|Transcript|intron_variant|||||INPP4B|protein_coding|||||||,C|ENSG00000109452|ENST00000507462|Transcript|intron_variant&NMD_transcript_variant|||||INPP4B|nonsense_mediated_decay|||||||;GR=0.574;PH=0.088;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-30.08,0,-85.88:4:99:45:14 0/1:-42.02,0,-58.12:2:99:37:16 4 144809866 . A G 483 PASS Source=Platypus;CSQ=G|ENSG00000197465|ENST00000437468|Transcript|intron_variant|||||GYPE|protein_coding|||||||,G|ENSG00000197465|ENST00000358615|Transcript|intron_variant|||||GYPE|protein_coding|YES||||||,G|ENSG00000197465|ENST00000506264|Transcript|intron_variant&NMD_transcript_variant|||||GYPE|nonsense_mediated_decay|||||||,G||ENSR00001251001|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.56;PH=0.968;PS=0.032;SD=0.972107 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.57,-191.7:1:99:53:0 1/0:-93.14,0,-82.94:0:99:60:31 4 150453313 . TAG - 1338 PASS Source=Platypus;CSQ=-|ENSG00000234828|ENST00000511993|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-526A4.1|lincRNA|YES||||||,-|ENSG00000234828|ENST00000506683|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-526A4.1|lincRNA|||||||,-||ENSR00001251701|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.0888;PH=0.001;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-216.8:2:99:61:0 1/0:-54.35,0,-85.55:1:99:46:18 4 160613755 . A G 2519 PASS Source=Platypus;CSQ=G|ENSG00000250488|ENST00000513718|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-6C14.1|lincRNA|YES||||||;GR=0.149;PH=0.166;PS=0.02;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-8.08,-100.3:5:81:28:0 1/0:-61.6,0,-53.5:4:99:34:18 4 161217587 . CAC - 621 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-4.75;PH=-1.59;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-149.9,-12.94,0:7:99:44:44 1/1:-150.7,-12.64,0:3:99:42:42 4 167058410 . T C 1767 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-3.85;PH=-0.782;PS=0 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:2:10:29,29:8,8 1/2:-1,-1,-1:6:18:42,42:11,11 4 172644469 . A G 180 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.131;PH=0.148;PS=0.175;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-6.62,-81.4:3:66:24:0 1/1:-173.9,-14.45,0:2:99:49:49 4 183687282 rs570959743 G A 356 PASS Source=Platypus;CSQ=A|ENSG00000218336|ENST00000511685|Transcript|intron_variant|||||TENM3|protein_coding|YES||||||,A|ENSG00000218336|ENST00000406950|Transcript|intron_variant|||||TENM3|protein_coding|||||||;GR=2.71;PH=1.089;PS=0.001;1000G=0.000599042 GT:GL:GOF:GQ:NR:NV 1/0:-66.65,0,-43.55:11:99:39:25 1/1:-130.7,-10.54,0:1:99:36:36 4 185727993 . T C 2562 PASS Source=Platypus;CSQ=C|ENSG00000151726|ENST00000504900|Transcript|intron_variant|||||ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000504342|Transcript|intron_variant|||||ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000515030|Transcript|intron_variant|||||ACSL1|protein_coding|YES||||||,C|ENSG00000151726|ENST00000513317|Transcript|upstream_gene_variant||||1051|ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000507295|Transcript|intron_variant|||||ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000437665|Transcript|intron_variant|||||ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000454703|Transcript|intron_variant|||||ACSL1|protein_coding|||||||,C|ENSG00000151726|ENST00000506733|Transcript|intron_variant&NMD_transcript_variant|||||ACSL1|nonsense_mediated_decay|||||||,C|ENSG00000151726|ENST00000281455|Transcript|intron_variant|||||ACSL1|protein_coding|||||||;GR=2.97;PH=0.762;PS=0.82 GT:GL:GOF:GQ:NR:NV 1/1:-239.3,-19.87,0:1:99:69:69 1/0:-92.14,0,-73.94:3:99:57:31 4 186222246 . C T 850 PASS Source=Platypus;CSQ=T|ENSG00000109762|ENST00000504273|Transcript|intron_variant|||||SNX25|protein_coding|YES||||||,T|ENSG00000109762|ENST00000264694|Transcript|intron_variant|||||SNX25|protein_coding|||||||,T|ENSG00000109762|ENST00000512853|Transcript|intron_variant&non_coding_transcript_variant|||||SNX25|processed_transcript|||||||;GR=-0.942;PH=-3.742;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-211.5,-17.44,0:2:99:60:60 1/0:-47.75,0,-95.35:5:99:49:19 4 190066910 . A G 478 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.48;PH=0.939;PS=0.006 GT:GL:GOF:GQ:NR:NV 1/1:-169.3,-13.82,0:1:99:47:47 1/0:-101.7,0,-87.3:1:99:62:32 5 4394766 . A G 1750 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.149;PH=0.166;PS=0.115;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-64.14,0,-109.14:2:99:63:27 0/0:0,-14.75,-180.3:3:99:52:0 5 11012456 . G A 2887 PASS Source=Platypus;CSQ=A|ENSG00000169862|ENST00000511377|Transcript|intron_variant|||||CTNND2|protein_coding|||||||,A|ENSG00000169862|ENST00000304623|Transcript|intron_variant|||||CTNND2|protein_coding|YES||||||,A|ENSG00000169862|ENST00000506324|Transcript|intron_variant&non_coding_transcript_variant|||||CTNND2|processed_transcript|||||||,A|ENSG00000169862|ENST00000513588|Transcript|intron_variant&NMD_transcript_variant|||||CTNND2|nonsense_mediated_decay|||||||,A|ENSG00000169862|ENST00000359640|Transcript|intron_variant|||||CTNND2|protein_coding|||||||,A|ENSG00000169862|ENST00000503622|Transcript|intron_variant|||||CTNND2|protein_coding|||||||,A|ENSG00000169862|ENST00000458100|Transcript|intron_variant|||||CTNND2|protein_coding|||||||,A|ENSG00000169862|ENST00000495388|Transcript|intron_variant&non_coding_transcript_variant|||||CTNND2|processed_transcript|||||||,A|ENSG00000169862|ENST00000504499|Transcript|intron_variant&NMD_transcript_variant|||||CTNND2|nonsense_mediated_decay|||||||;GR=0.663;PH=0.156;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-62.91,0,-60.01:3:99:43:21 1/0:-43.25,0,-99.85:2:99:48:17 5 12468829 . C T 1230 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.225;PH=0.3;PS=0.212;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.95,-188.9:2:99:54:0 1/1:-178.9,-14.73,0:4:99:48:48 5 13469142 . C T 623 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.755;PH=-1.289;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-92.56,0,-87.36:1:99:64:31 0/1:-71.35,0,-85.45:2:99:55:27 5 15611230 . A G 907 PASS Source=Platypus;CSQ=G|ENSG00000183580|ENST00000329673|Transcript|upstream_gene_variant||||4861|FBXL7|protein_coding|||||||,G|ENSG00000250250|ENST00000509228|Transcript|upstream_gene_variant||||3872|CTD-2350J17.1|antisense|YES||||||,G|ENSG00000250250|ENST00000510456|Transcript|upstream_gene_variant||||3773|CTD-2350J17.1|antisense|||||||,G|ENSG00000183580|ENST00000510662|Transcript|intron_variant|||||FBXL7|protein_coding|||||||,G|ENSG00000183580|ENST00000504595|Transcript|intron_variant|||||FBXL7|protein_coding|YES||||||;GR=-2.83;PH=-0.756;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-21.07,-247.9:2:99:74:0 1/1:-194,-16.37,0:6:99:56:56 5 16237760 . T C 77 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=2.53;PH=0.755;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-72.84,0,-93.04:2:99:58:28 0/1:-85.64,0,-80.74:3:99:58:29 5 16270358 . AGGA - 2792 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.524;PH=-0.152;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-88.7,-7.53,0:3:75:26:25 1/1:-95.9,-8.03,0:3:80:29:29 5 18655583 . C T 478 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.158;PH=0.202;PS=0.228;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-212.4,-18.64,0:63:99:65:65 1/0:-71.39,0,-68.09:42:99:47:23 5 22078425 . G A 1780 PASS Source=Platypus;CSQ=A|ENSG00000154162|ENST00000522262|Transcript|intron_variant|||||CDH12|protein_coding|||||||,A|ENSG00000154162|ENST00000504376|Transcript|intron_variant|||||CDH12|protein_coding|||||||,A|ENSG00000154162|ENST00000382254|Transcript|intron_variant|||||CDH12|protein_coding|YES||||||,A|ENSG00000154162|ENST00000517378|Transcript|intron_variant&non_coding_transcript_variant|||||CDH12|retained_intron|||||||,A|ENSG00000154162|ENST00000518209|Transcript|downstream_gene_variant||||168|CDH12|processed_transcript|||||||,A|ENSG00000154162|ENST00000521745|Transcript|downstream_gene_variant||||385|CDH12|processed_transcript|||||||;GR=4.07;PH=2.597;PS=0.99;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-75.41,0,-30.01:31:99:35:22 1/0:-88.49,0,-28.39:27:99:38:25 5 22459466 . A G 723 PASS Source=Platypus;CSQ=G|ENSG00000154162|ENST00000504376|Transcript|intron_variant|||||CDH12|protein_coding|||||||,G|ENSG00000154162|ENST00000382254|Transcript|intron_variant|||||CDH12|protein_coding|YES||||||,G|ENSG00000154162|ENST00000520668|Transcript|intron_variant&non_coding_transcript_variant|||||CDH12|processed_transcript|||||||;GR=1.15;PH=0.104;PS=0.005 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.19,-154.5:2:99:48:0 1/1:-174.4,-15.33,0:3:99:55:55 5 23378739 . G A 337 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;PH=0.119;PS=0.169;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.78,-234.7:1:99:70:0 1/0:-74.99,0,-110.39:4:99:55:22 5 27022942 . AGAG - 2104 PASS Source=Platypus;CSQ=-|ENSG00000113100|ENST00000511822|Transcript|intron_variant&feature_truncation|||||CDH9|protein_coding|||||||,-|ENSG00000113100|ENST00000231021|Transcript|intron_variant&feature_truncation|||||CDH9|protein_coding|YES||||||,-|ENSG00000113100|ENST00000513289|Transcript|intron_variant&feature_truncation|||||CDH9|protein_coding|||||||,-|ENSG00000113100|ENST00000505045|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CDH9|retained_intron|||||||;GR=0.664;PH=0.116;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-70.88,0,-70.48:2:99:48:24 0/0:0,-14.11,-166.2:4:99:49:0 5 36546207 . T C 1128 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.235;PH=0.263;PS=0.205;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-6.06,-300:47:61:56:13 0/1:-15.87,0,-300:88:99:31:15 5 42089066 . GGCC - 2121 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.158;PH=0.202;PS=0.05;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-35.76,-2.98,0:16:30:19:8 0/0:0,-1.54,-80.96:20:15:46:1 5 44503071 . A G 2326 PASS Source=Platypus;CSQ=G|ENSG00000249203|ENST00000505706|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-473L15.3|lincRNA|YES||||||,G|ENSG00000249203|ENST00000510758|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-473L15.3|lincRNA|||||||;GR=1.73;PH=1.054;PS=0.014 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-217.7:2:99:61:0 0/1:-80.87,0,-70.57:2:99:53:28 5 45183117 . C T 700 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.245;PH=0.104;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-57.54,0,-99.24:3:99:56:23 0/0:0,-15.03,-183.2:1:99:53:0 5 49451028 . G A 1711 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;REPMASK=Satellite GT:GL:GOF:GQ:NR:NV 0/1:-67.02,0,-96.12:1:99:57:23 0/0:0,-9.03,-111.4:0:90:32:0 5 55648768 . TGAA - 1704 PASS Source=Platypus;CSQ=-||ENSR00001280519|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,-||||intergenic_variant|||||||||||||;GR=2.42;PH=0.747;PS=0.048 GT:GL:GOF:GQ:NR:NV 1/0:-64.98,0,-83.08:3:99:55:25 1/1:-173.8,-14.34,0:3:99:49:49 5 56633812 . T C 1672 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.916;PH=-0.617;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-21.34,0,-76.94:8:99:36:7 1/0:-24.54,0,-79.32:6:99:41:9 5 62848071 . C T 2549 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.351;PH=0.399;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-52.22,0,-89.62:5:99:49:19 0/0:0,-14.15,-164.2:2:99:49:0 5 66185789 . A G 1141 PASS Source=Platypus;CSQ=G|ENSG00000069020|ENST00000403666|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000404260|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000490016|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000411628|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000406374|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000403625|Transcript|intron_variant|||||MAST4|protein_coding|YES||||||,G|ENSG00000069020|ENST00000452953|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000434115|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000450827|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000432817|Transcript|intron_variant|||||MAST4|protein_coding|||||||,G|ENSG00000069020|ENST00000470421|Transcript|intron_variant&non_coding_transcript_variant|||||MAST4|retained_intron|||||||,G|ENSG00000069020|ENST00000406039|Transcript|intron_variant|||||MAST4|protein_coding|||||||;GR=-0.808;PH=-0.075;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.6,-148.9:0:99:45:0 0/1:-94.03,0,-123.73:17:99:75:33 5 66515338 . T C 1772 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.0465;PH=0.115;PS=0.028;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-51.78,0,-94.18:3:99:52:20 0/1:-61.96,0,-61.46:0:99:42:20 5 69795560 . GT - 1390 PASS Source=Platypus;CSQ=-|ENSG00000253333|ENST00000509969|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-497H16.8|unprocessed_pseudogene|YES||||||;PH=0.064;PS=0.119;SD=0.996984 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.21,-161.3:1:99:47:0 1/0:-72.93,0,-76.33:4:99:52:26 5 71815911 . T C 81 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.23;PH=0.343;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-100.7,-8.7,0:17:87:38:35 0/1:-44.71,0,-65.41:17:99:49:21 5 72977263 . TCA - 2650 PASS Source=Platypus;CSQ=-|ENSG00000214944|ENST00000437974|Transcript|upstream_gene_variant||||3392|ARHGEF28|protein_coding|||||||,-|ENSG00000214944|ENST00000513042|Transcript|intron_variant&feature_truncation|||||ARHGEF28|protein_coding|||||||,-|ENSG00000214944|ENST00000287898|Transcript|intron_variant&feature_truncation|||||ARHGEF28|protein_coding|||||||,-|ENSG00000214944|ENST00000509848|Transcript|intron_variant&feature_truncation|||||ARHGEF28|protein_coding|||||||,-|ENSG00000214944|ENST00000545377|Transcript|intron_variant&feature_truncation|||||ARHGEF28|protein_coding|YES||||||,-|ENSG00000214944|ENST00000426542|Transcript|upstream_gene_variant||||3392|ARHGEF28|protein_coding|||||||,-|ENSG00000214944|ENST00000296794|Transcript|intron_variant&feature_truncation|||||ARHGEF28|protein_coding|||||||;GR=0.537;PH=0.454;PS=0.462;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/1:-88.65,0,-51.45:1:99:47:29 0/1:-89.35,0,-50.65:0:99:46:28 5 75805765 . A G 1068 PASS Source=Platypus;CSQ=G|ENSG00000145703|ENST00000514350|Transcript|intron_variant|||||IQGAP2|protein_coding|||||||,G|ENSG00000250574|ENST00000505876|Transcript|upstream_gene_variant||||500|CTD-2275D10.2|processed_pseudogene|YES||||||,G|ENSG00000145703|ENST00000274364|Transcript|intron_variant|||||IQGAP2|protein_coding|YES||||||,G|ENSG00000145703|ENST00000379730|Transcript|intron_variant|||||IQGAP2|protein_coding|||||||;GR=1.37;PH=1.206;PS=0.288 GT:GL:GOF:GQ:NR:NV 0/0:0,-21.05,-243:0:99:72:0 1/1:-179.1,-14.75,0:1:99:50:50 5 78480043 . C T 2280 PASS Source=Platypus;CSQ=T|ENSG00000132837|ENST00000518707|Transcript|intron_variant&non_coding_transcript_variant|||||DMGDH|processed_transcript|||||||,T|ENSG00000132837|ENST00000520388|Transcript|intron_variant&non_coding_transcript_variant|||||DMGDH|processed_transcript|||||||;GR=-1.97;PH=-0.082;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/1:-232.7,-19.27,0:1:99:67:67 1/1:-194.5,-15.76,0:7:99:55:54 5 88517719 . A G 1722 PASS Source=Platypus;CSQ=G|ENSG00000248309|ENST00000512585|Transcript|intron_variant&non_coding_transcript_variant|||||MEF2C-AS1|antisense|||||||,G|ENSG00000248309|ENST00000514092|Transcript|intron_variant&non_coding_transcript_variant|||||MEF2C-AS1|antisense|||||||;PH=0.103;PS=0.211;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-56.76,0,-48.76:6:99:43:22 0/0:0,-6.62,-80.1:14:66:30:0 5 89894747 . C T 852 PASS Source=Platypus;CSQ=T|ENSG00000164199|ENST00000405460|Transcript|intron_variant|||||GPR98|protein_coding|YES||||||,T|ENSG00000164199|ENST00000508842|Transcript|intron_variant|||||GPR98|protein_coding|||||||;GR=-0.705;PH=-0.197;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-88.55,0,-73.35:2:99:56:31 0/0:0,-14.15,-173:1:99:49:0 5 90980165 . G A 1996 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.13;PH=-0.269;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.96,-222.9:7:99:66:0 1/1:-140.2,-11.99,0:5:99:41:41 5 94131115 . T C 869 PASS Source=Platypus;CSQ=C|ENSG00000175471|ENST00000429576|Transcript|intron_variant|||||MCTP1|protein_coding|||||||,C|ENSG00000175471|ENST00000515393|Transcript|intron_variant|||||MCTP1|protein_coding|YES||||||,C|ENSG00000175471|ENST00000312216|Transcript|intron_variant|||||MCTP1|protein_coding|||||||,C|ENSG00000175471|ENST00000508509|Transcript|intron_variant|||||MCTP1|protein_coding|||||||,C|ENSG00000249175|ENST00000513849|Transcript|downstream_gene_variant||||1811|CTC-484P3.3|antisense|YES||||||,C|ENSG00000175471|ENST00000512425|Transcript|downstream_gene_variant||||3675|MCTP1|protein_coding|||||||,C|ENSG00000175471|ENST00000505078|Transcript|intron_variant|||||MCTP1|protein_coding|||||||;GR=-6.63;PH=-1.272;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-87.56,0,-97.66:1:99:65:32 0/1:-72.55,0,-86.25:1:99:54:26 5 94676995 . CACC - 37 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.064;PS=0.165;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-61.66,0,-52.76:3:99:49:28 1/0:-25.39,0,-74.69:6:99:39:11 5 111481725 . G A 2144 PASS Source=Platypus;CSQ=A|ENSG00000129595|ENST00000507810|Transcript|intron_variant&non_coding_transcript_variant|||||EPB41L4A|processed_transcript|||||||,A||ENSR00001287518|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.39;PH=-0.313;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-91.86,0,-94.96:2:99:63:30 0/1:-61.25,0,-98.35:1:99:52:21 5 112295409 . G A 1133 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.354;PH=0.399;PS=0.061;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-140.8,-10.37,0:5:99:45:43 1/1:-201.2,-16.52,0:1:99:57:57 5 115114770 . TT - 220 PASS Source=Platypus;CSQ=-|ENSG00000222598|ENST00000410666|Transcript|upstream_gene_variant||||4571|RNU2-49P|snRNA|YES||||||;GR=0.0199;PH=-0.269;PS=0.002;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/0:-84.46,0,-82.56:3:99:46:19 0/0:0,-12.34,-234.4:0:99:50:0 5 116611406 . G A 523 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.84;PH=-0.507;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-18.06,-220.6:3:99:61:0 1/0:-75.88,0,-101.48:0:99:61:25 5 117018050 . T C 1728 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.74;PH=0.391;PS=0.012;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:9:57:17,17:11,11 1/2:-1,-1,-1:9:99:29,29:15,15 5 119698074 . A G 1022 PASS Source=Platypus;CSQ=G|ENSG00000261036|ENST00000569928|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-574H6.1|lincRNA|YES||||||;GR=0.354;PH=0.071;PS=0.01 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.64,-155.2:21:99:43:0 1/0:-85.18,0,-76.68:29:99:56:29 5 128550449 . TT - 1369 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.103;PS=0.204;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-171.5,-14.73,0:3:99:52:51 1/1:-133,-11.12,0:2:99:40:40 5 134755230 . GC - 2088 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.427;PH=0.458;PS=0.048;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-211.9,-18.3,0:1:99:62:62 1/0:-99.17,0,-47.57:0:99:48:31 5 135195587 . TGG - 824 PASS Source=Platypus;CSQ=-|ENSG00000145832|ENST00000420621|Transcript|intron_variant&feature_truncation|||||SLC25A48|protein_coding|||||||,-|ENSG00000145832|ENST00000425402|Transcript|intron_variant&feature_truncation|||||SLC25A48|protein_coding|||||||,-|ENSG00000145832|ENST00000462340|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||SLC25A48|nonsense_mediated_decay|||||||,-|ENSG00000145832|ENST00000433282|Transcript|intron_variant&feature_truncation|||||SLC25A48|protein_coding|||||||,-|ENSG00000145832|ENST00000412661|Transcript|intron_variant&feature_truncation|||||SLC25A48|protein_coding|YES||||||,-|ENSG00000145832|ENST00000274513|Transcript|intron_variant&feature_truncation|||||SLC25A48|protein_coding|||||||;GR=0.235;PH=0.263;PS=0.03;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-18.34,-223.7:24:99:64:0 0/1:-83.49,0,-57.09:22:99:48:27 5 142459686 . A G 1112 PASS Source=Platypus;CSQ=G|ENSG00000145819|ENST00000274498|Transcript|intron_variant|||||ARHGAP26|protein_coding|YES||||||,G|ENSG00000145819|ENST00000418236|Transcript|intron_variant|||||ARHGAP26|protein_coding|||||||,G|ENSG00000145819|ENST00000443674|Transcript|intron_variant|||||ARHGAP26|protein_coding|||||||,G|ENSG00000145819|ENST00000378004|Transcript|intron_variant|||||ARHGAP26|protein_coding|||||||;GR=2.9;PH=1.574;PS=0.045 GT:GL:GOF:GQ:NR:NV 0/1:-67.59,0,-68.39:24:99:48:24 1/1:-179.8,-15.05,0:23:99:51:50 5 150288710 . A G 1882 PASS Source=Platypus;CSQ=G|ENSG00000145908|ENST00000418587|Transcript|upstream_gene_variant||||4165|ZNF300|protein_coding|||||||,G|ENSG00000145908|ENST00000427179|Transcript|upstream_gene_variant||||4359|ZNF300|protein_coding|||||||,G|ENSG00000145908|ENST00000274599|Transcript|upstream_gene_variant||||4165|ZNF300|protein_coding|||||||,G|ENSG00000145908|ENST00000394226|Transcript|upstream_gene_variant||||4170|ZNF300|protein_coding|||||||,G|ENSG00000145908|ENST00000446148|Transcript|upstream_gene_variant||||4165|ZNF300|protein_coding|YES||||||;GR=1.26;PH=0.84;PS=0.026;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-99.93,0,-104.53:1:99:69:35 0/1:-85.85,0,-61.95:1:99:50:29 5 151065677 . T C 2511 PASS Source=Platypus;CSQ=C|ENSG00000113140|ENST00000522348|Transcript|intron_variant|||||SPARC|protein_coding|||||||,C|ENSG00000249035|ENST00000518905|Transcript|intron_variant&non_coding_transcript_variant|||||CTB-113P19.1|antisense|||||||,C|ENSG00000113140|ENST00000538026|Transcript|intron_variant|||||SPARC|protein_coding|||||||,C|ENSG00000113140|ENST00000539687|Transcript|upstream_gene_variant||||886|SPARC|protein_coding|||||||,C|ENSG00000113140|ENST00000231061|Transcript|intron_variant|||||SPARC|protein_coding|YES||||||,C|ENSG00000113140|ENST00000521327|Transcript|intron_variant&non_coding_transcript_variant|||||SPARC|retained_intron|||||||,C|ENSG00000113140|ENST00000521569|Transcript|intron_variant|||||SPARC|protein_coding|||||||,C|ENSG00000249035|ENST00000510576|Transcript|intron_variant&non_coding_transcript_variant|||||CTB-113P19.1|antisense|YES||||||,C||ENSR00001294210|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-0.619;PH=-0.105;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-84.27,0,-75.57:4:99:56:30 0/0:0,-12.62,-149.4:0:99:44:0 5 159293000 . T C 2900 PASS Source=Platypus;CSQ=C|ENSG00000253311|ENST00000522627|Transcript|intron_variant&non_coding_transcript_variant|||||AC011343.1|lincRNA|YES||||||;GR=3;PH=1.184;PS=0.003 GT:GL:GOF:GQ:NR:NV ./.:-0.3,0,-0.3:6:3:0:0 1/1:-29.3,-2.11,0:4:21:9:9 5 159942758 . AGCT - 2252 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.1;PH=-0.188;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.56,-204.2:5:99:56:0 1/0:-56.65,0,-85.25:1:99:47:20 5 162754508 . C T 746 PASS Source=Platypus;CSQ=T|ENSG00000250061|ENST00000503504|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-541P9.3|antisense|||||||,T|ENSG00000250061|ENST00000458002|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-541P9.3|antisense|||||||;GR=0.235;PH=0.308;PS=0.171;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-100.57,0,-78.67:4:99:63:34 1/0:-57.76,0,-67.46:2:99:42:20 5 166461300 . GTC - 2970 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.31;PH=-0.453;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-77.7,-3.61,0:248:36:14:11 1/0:-24.02,0,-90.12:46:99:22:5 5 167182707 . A G 232 PASS Source=Platypus;CSQ=G|ENSG00000145934|ENST00000545108|Transcript|intron_variant|||||TENM2|protein_coding|||||||,G|ENSG00000145934|ENST00000520394|Transcript|intron_variant|||||TENM2|protein_coding|||||||,G|ENSG00000145934|ENST00000519204|Transcript|intron_variant|||||TENM2|protein_coding|||||||,G|ENSG00000145934|ENST00000518659|Transcript|intron_variant|||||TENM2|protein_coding|YES||||||,G|ENSG00000145934|ENST00000520393|Transcript|intron_variant&non_coding_transcript_variant|||||TENM2|processed_transcript|||||||,G||ENSR00001416203|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.71;PH=0.345;PS=0.099 GT:GL:GOF:GQ:NR:NV 1/1:-170.3,-14.12,0:3:99:51:51 0/0:0,-15.05,-185.4:2:99:53:0 5 174458858 . T C 1972 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-2.84;PH=-0.815;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-72.81,0,-58.51:6:99:57:30 0/1:-70.97,0,-80.37:2:99:60:29 6 5636932 . G A 678 PASS Source=Platypus;CSQ=A|ENSG00000145982|ENST00000324331|Transcript|intron_variant|||||FARS2|protein_coding|YES||||||,A|ENSG00000145982|ENST00000274680|Transcript|intron_variant|||||FARS2|protein_coding|||||||;GR=-2.4;PH=-0.647;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-218.1,-18.57,0:2:99:63:63 1/0:-105.44,0,-55.24:3:99:55:34 6 12572358 . C T 1656 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-3.83;PH=-0.961;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.79,-199.2:2:99:57:0 0/1:-66.34,0,-56.54:2:99:40:22 6 17461129 . A G 463 PASS Source=Platypus;CSQ=G|ENSG00000112186|ENST00000465994|Transcript|intron_variant|||||CAP2|protein_coding|||||||,G|ENSG00000112186|ENST00000378990|Transcript|intron_variant|||||CAP2|protein_coding|||||||,G|ENSG00000112186|ENST00000489374|Transcript|intron_variant|||||CAP2|protein_coding|||||||,G|ENSG00000112186|ENST00000229922|Transcript|intron_variant|||||CAP2|protein_coding|YES||||||,G|ENSG00000112186|ENST00000476263|Transcript|intron_variant&NMD_transcript_variant|||||CAP2|nonsense_mediated_decay|||||||,G|ENSG00000112186|ENST00000479291|Transcript|intron_variant&NMD_transcript_variant|||||CAP2|nonsense_mediated_decay|||||||,G|ENSG00000112186|ENST00000493172|Transcript|intron_variant|||||CAP2|protein_coding|||||||;GR=0.149;PH=0.166;PS=0.045;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-300,0,-300:27:99:44:18 0/0:0,-15.05,-300:3:99:49:0 6 17484074 . AG - 1799 PASS Source=Platypus;CSQ=-|ENSG00000112186|ENST00000465994|Transcript|intron_variant&feature_truncation|||||CAP2|protein_coding|||||||,-|ENSG00000112186|ENST00000378990|Transcript|intron_variant&feature_truncation|||||CAP2|protein_coding|||||||,-|ENSG00000112186|ENST00000489374|Transcript|intron_variant&feature_truncation|||||CAP2|protein_coding|||||||,-|ENSG00000112186|ENST00000229922|Transcript|intron_variant&feature_truncation|||||CAP2|protein_coding|YES||||||,-|ENSG00000112186|ENST00000476263|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CAP2|nonsense_mediated_decay|||||||,-|ENSG00000112186|ENST00000479291|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||CAP2|nonsense_mediated_decay|||||||,-|ENSG00000112186|ENST00000493172|Transcript|intron_variant&feature_truncation|||||CAP2|protein_coding|||||||;GR=0.582;PH=0.13;PS=0 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:18:99:50,50:18,50 1/2:-1,-1,-1:17:99:57,57:14,57 6 24681906 . CAG - 2072 PASS Source=Platypus;CSQ=-|ENSG00000112304|ENST00000230048|Transcript|intron_variant&feature_truncation|||||ACOT13|protein_coding|YES||||||,-|ENSG00000112304|ENST00000537591|Transcript|intron_variant&feature_truncation|||||ACOT13|protein_coding|||||||;PH=0.119;PS=0.01;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-180.6,-15.65,0:4:99:55:55 1/1:-175,-14.7,0:0:99:51:51 6 26065344 . GGC - 29 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.91;PH=-0.812;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-21.94,-266.1:2:99:78:0 1/0:-81.96,0,-77.86:3:99:57:30 6 36438796 . CAGA - 165 PASS Source=Platypus;CSQ=-|ENSG00000112078|ENST00000544295|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||,-|ENSG00000112078|ENST00000474988|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||KCTD20|processed_transcript|||||||,-|ENSG00000112078|ENST00000460983|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||,-|ENSG00000112078|ENST00000449081|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||,-|ENSG00000112078|ENST00000498267|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||,-|ENSG00000112078|ENST00000536244|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||,-|ENSG00000112078|ENST00000373731|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|YES||||||,-|ENSG00000112078|ENST00000481911|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||KCTD20|nonsense_mediated_decay|||||||,-|ENSG00000112078|ENST00000265344|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||KCTD20|nonsense_mediated_decay|||||||,-|ENSG00000112078|ENST00000483557|Transcript|intron_variant&feature_truncation|||||KCTD20|protein_coding|||||||;GR=-0.47;PH=-0.671;PS=0.009;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-246.4,-20.17,0:1:99:68:68 1/1:-187.4,-14.75,0:0:99:51:50 6 39821984 . AA - 2498 PASS Source=Platypus;CSQ=-|ENSG00000146122|ENST00000405961|Transcript|intron_variant&feature_truncation|||||DAAM2|protein_coding|||||||,-|ENSG00000146122|ENST00000274867|Transcript|intron_variant&feature_truncation|||||DAAM2|protein_coding|||||||,-|ENSG00000146122|ENST00000475489|Transcript|upstream_gene_variant||||2038|DAAM2|retained_intron|||||||,-|ENSG00000146122|ENST00000494405|Transcript|upstream_gene_variant||||2038|DAAM2|processed_transcript|||||||,-|ENSG00000146122|ENST00000398904|Transcript|intron_variant&feature_truncation|||||DAAM2|protein_coding|YES||||||,-|ENSG00000146122|ENST00000538976|Transcript|intron_variant&feature_truncation|||||DAAM2|protein_coding|||||||;GR=0.699;PH=-0.093;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.44,-207.7:4:99:62:0 1/0:-88.35,0,-77.35:1:99:55:30 6 41198005 . C T 2531 PASS Source=Platypus;CSQ=T|ENSG00000188056|ENST00000461240|Transcript|intron_variant&NMD_transcript_variant|||||TREML4|nonsense_mediated_decay|||||||,T|ENSG00000188056|ENST00000448827|Transcript|intron_variant|||||TREML4|protein_coding|||||||,T|ENSG00000188056|ENST00000341495|Transcript|intron_variant|||||TREML4|protein_coding|YES||||||;GR=-1.93;PH=-0.539;PS=0;SD=0.921412 GT:GL:GOF:GQ:NR:NV 1/1:-190.8,-15.86,0:2:99:55:55 1/1:-174.5,-14.45,0:2:99:51:51 6 49333697 . T C 1644 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.189;PH=0.25;PS=0.035;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-103.8,-8.73,0:16:87:40:38 0/0:0,-13.5,-158.3:1:99:48:0 6 57412493 . GC - 2013 PASS Source=Platypus;CSQ=-|ENSG00000146143|ENST00000389488|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PRIM2|processed_transcript|||||||,-|ENSG00000146143|ENST00000607273|Transcript|intron_variant&feature_truncation|||||PRIM2|protein_coding|YES||||||,-|ENSG00000146143|ENST00000550475|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PRIM2|processed_transcript|||||||,-||ENSR00001219388|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-3.75;PH=-1.037;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-228.5,-15.05,0:1:99:54:46 1/1:-191.4,-12.64,0:1:99:42:37 6 63977121 . G A 18 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-1.34;PH=-4.902;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-4.82,-60.2:12:48:17:0 1/1:-151.3,-12.64,0:5:99:42:42 6 70958472 . A G 2836 PASS Source=Platypus;CSQ=G|ENSG00000112280|ENST00000360859|Transcript|intron_variant&non_coding_transcript_variant|||||COL9A1|processed_transcript|||||||,G|ENSG00000112280|ENST00000493682|Transcript|intron_variant&non_coding_transcript_variant|||||COL9A1|retained_intron|||||||,G|ENSG00000112280|ENST00000370499|Transcript|intron_variant|||||COL9A1|protein_coding|||||||,G|ENSG00000112280|ENST00000320755|Transcript|intron_variant|||||COL9A1|protein_coding|||||||,G|ENSG00000112280|ENST00000489861|Transcript|downstream_gene_variant||||3397|COL9A1|retained_intron|||||||,G|ENSG00000112280|ENST00000489611|Transcript|intron_variant&non_coding_transcript_variant|||||COL9A1|processed_transcript|||||||,G|ENSG00000112280|ENST00000447041|Transcript|intron_variant&non_coding_transcript_variant|||||COL9A1|processed_transcript|||||||,G|ENSG00000112280|ENST00000357250|Transcript|intron_variant|||||COL9A1|protein_coding|YES||||||,G|ENSG00000112280|ENST00000486080|Transcript|upstream_gene_variant||||2466|COL9A1|processed_transcript|||||||;GR=-0.313;PH=-0.035;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-300,0,-300:5:99:40:17 1/1:-300,-11.44,0:4:99:38:31 6 71951162 . CCC - 1193 PASS Source=Platypus;CSQ=-|ENSG00000232295|ENST00000602418|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-154D6.1|antisense|||||||;GR=0.149;PH=0.192;PS=0.011;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-147.7,-12.64,0:15:99:45:45 1/1:-182.1,-14.94,0:2:99:51:51 6 74489959 . G A 972 PASS Source=Platypus;CSQ=A|ENSG00000156535|ENST00000287097|Transcript|intron_variant|||||CD109|protein_coding|YES||||||,A|ENSG00000156535|ENST00000437994|Transcript|intron_variant|||||CD109|protein_coding|||||||,A|ENSG00000156535|ENST00000422508|Transcript|intron_variant|||||CD109|protein_coding|||||||;GR=-3.65;PH=-0.522;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-125,-11.05,0:3:99:39:38 0/1:-46.17,0,-43.37:2:99:31:17 6 76718317 . A G 2976 PASS Source=Platypus;CSQ=G|ENSG00000112706|ENST00000369950|Transcript|intron_variant|||||IMPG1|protein_coding|YES||||||,G|ENSG00000112706|ENST00000369963|Transcript|intron_variant|||||IMPG1|protein_coding|||||||;GR=1.59;PH=0.45;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-192.5,-15.86,0:10:99:54:54 1/1:-165,-14.36,0:3:99:49:49 6 81218677 . T C 1519 alleleBias Source=Platypus;CSQ=C||ENSR00001221117|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=2.22;PH=1.284;PS=0.037;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-91.64,0,-93.64:3:99:63:31 1/0:-71.02,0,-34.92:1:99:35:22 6 87625723 . T C 2605 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.647;PH=0.166;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.21,-199.2:4:99:63:0 1/0:-74.45,0,-58.15:2:99:45:24 6 93016037 . T C 1274 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;PH=0.056;PS=0.425;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-229.3,-15.35,0:2:99:54:46 1/1:-208.5,-13.85,0:1:99:45:38 6 96053506 . A G 2894 PASS Source=Platypus;CSQ=G|ENSG00000172469|ENST00000358812|Transcript|intron_variant|||||MANEA|protein_coding|YES||||||,G|ENSG00000172469|ENST00000474553|Transcript|intron_variant&non_coding_transcript_variant|||||MANEA|processed_transcript|||||||;GR=3.56;PH=0.489;PS=0.018 GT:GL:GOF:GQ:NR:NV 0/1:-5.16,0,-5.79:9:51:33:9 0/1:-4.01,0,-6.01:5:40:43:9 6 99015125 . G A 15 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.225;PH=0.3;PS=0.007;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-7.72,-97.4:2:77:49:4 1/0:-25.21,0,-50.61:13:99:47:10 6 112775706 . GT - 2542 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.869;PH=-0.272;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-16.56,-200.5:3:99:58:0 1/1:-196.6,-16.26,0:1:99:55:55 6 114530206 . A G 1232 PASS Source=Platypus;CSQ=G|ENSG00000249853|ENST00000312719|Transcript|intron_variant|||||HS3ST5|protein_coding|YES||||||,G|ENSG00000228624|ENST00000523087|Transcript|intron_variant&non_coding_transcript_variant|||||RP3-399L15.3|antisense|||||||,G|ENSG00000228624|ENST00000519104|Transcript|intron_variant&non_coding_transcript_variant|||||RP3-399L15.3|antisense|YES||||||;GR=2.5;PH=0.587;PS=0.032 GT:GL:GOF:GQ:NR:NV 0/1:-150.53,0,-243.13:14:99:74:44 0/0:0,-17.16,-300:4:99:62:0 6 131736221 . T C 2355 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.331;PH=-0.063;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-81.86,0,-100.96:9:99:62:28 0/0:0,-15.62,-188.1:2:99:56:0 6 134776331 . C T 21 PASS Source=Platypus;CSQ=T|ENSG00000236700|ENST00000431422|Transcript|intron_variant&non_coding_transcript_variant|||||LINC01010|lincRNA|YES||||||,T|ENSG00000231971|ENST00000417483|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-557H15.3|lincRNA|YES||||||,T|ENSG00000231971|ENST00000422736|Transcript|upstream_gene_variant||||612|RP11-557H15.3|lincRNA|||||||,T||ENSR00001500252|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.94;PH=-1.609;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-90.2,-7.98,0:11:80:39:37 1/1:-109,-9.33,0:3:93:46:44 6 138923043 . AAT - 48 PASS Source=Platypus;CSQ=-|ENSG00000135540|ENST00000468095|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NHSL1|retained_intron|||||||,-|ENSG00000135540|ENST00000491526|Transcript|intron_variant&feature_truncation|||||NHSL1|protein_coding|||||||;GR=-2.09;PH=-0.48;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-164.4,-13.83,0:11:99:48:48 1/1:-204.6,-16.56,0:13:99:56:56 6 144823473 . GC - 662 PASS Source=Platypus;CSQ=-|ENSG00000152818|ENST00000367545|Transcript|intron_variant&feature_truncation|||||UTRN|protein_coding|YES||||||;GR=0.39;PH=0.453;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-30.1,-2.03,0:25:20:11:6 1/0:-14.1,0,-1.3:12:13:11:3 6 145408018 . AG - 721 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.0788;PH=0.016;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-173.7,-13.85,0:8:99:49:49 0/1:-79.68,0,-79.78:2:99:52:25 6 147885577 . ATCA - 599 PASS Source=Platypus;CSQ=-|ENSG00000203727|ENST00000566741|Transcript|intron_variant&feature_truncation|||||SAMD5|protein_coding|||||||,-|ENSG00000203727|ENST00000367474|Transcript|frameshift_variant&feature_truncation|509-512|169-170|SS/X||SAMD5|protein_coding|YES||||||;GR=-0.299;PH=-0.195;PS=0.997;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-81.38,0,-84.38:2:99:58:27 1/0:-68.36,0,-54.36:2:99:45:26 6 149386949 . T C 994 PASS Source=Platypus;CSQ=C|ENSG00000111962|ENST00000367463|Transcript|intron_variant|||||UST|protein_coding|YES||||||,C|ENSG00000111962|ENST00000466695|Transcript|upstream_gene_variant||||363|UST|processed_transcript|||||||;GR=3.29;PH=0.804;PS=0.892 GT:GL:GOF:GQ:NR:NV 1/0:-179.58,0,-202.28:4:99:59:27 0/0:0,-17.76,-300:6:99:61:0 6 152733596 . C T 2679 PASS Source=Platypus;CSQ=T|ENSG00000131018|ENST00000423061|Transcript|intron_variant|||||SYNE1|protein_coding|||||||,T|ENSG00000131018|ENST00000535081|Transcript|upstream_gene_variant||||3157|SYNE1|retained_intron|||||||,T|ENSG00000131018|ENST00000448038|Transcript|intron_variant|||||SYNE1|protein_coding|||||||,T|ENSG00000131018|ENST00000367255|Transcript|intron_variant|||||SYNE1|protein_coding|YES||||||,T|ENSG00000131018|ENST00000461872|Transcript|intron_variant&non_coding_transcript_variant|||||SYNE1|retained_intron|||||||,T|ENSG00000202044|ENST00000365174|Transcript|downstream_gene_variant||||2067|RNA5SP223|rRNA|YES||||||,T|ENSG00000131018|ENST00000341594|Transcript|intron_variant|||||SYNE1|protein_coding|||||||,T|ENSG00000131018|ENST00000265368|Transcript|intron_variant|||||SYNE1|protein_coding|||||||;GR=-1.73;PH=-0.592;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-127.1,-10.24,0:2:99:37:37 1/1:-144.2,-12.04,0:1:99:41:41 6 153689977 . TAA - 2993 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.149;PH=0.166;PS=0.07;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-166.1,-13.53,0:11:99:49:49 0/1:-63.46,0,-67.66:1:99:44:21 6 157276935 . CTTA - 680 PASS Source=Platypus;CSQ=-|ENSG00000049618|ENST00000319584|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|||||||,-|ENSG00000049618|ENST00000367148|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|||||||,-|ENSG00000049618|ENST00000350026|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|||||||,-|ENSG00000049618|ENST00000414678|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|||||||,-|ENSG00000049618|ENST00000452544|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||ARID1B|retained_intron|||||||,-|ENSG00000049618|ENST00000275248|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|||||||,-|ENSG00000049618|ENST00000346085|Transcript|intron_variant&feature_truncation|||||ARID1B|protein_coding|YES||||||,-||ENSR00001501895|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.29;PH=0.887;PS=0.117 GT:GL:GOF:GQ:NR:NV 0/0:0,-11.11,-168.5:3:99:52:1 1/0:-63.7,0,-36.1:5:99:37:23 6 161422496 . TGA - 1687 PASS Source=Platypus;CSQ=-|ENSG00000085511|ENST00000542952|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MAP3K4|nonsense_mediated_decay|||||||,-|ENSG00000085511|ENST00000366919|Transcript|intron_variant&feature_truncation|||||MAP3K4|protein_coding|||||||,-|ENSG00000085511|ENST00000348824|Transcript|intron_variant&feature_truncation|||||MAP3K4|protein_coding|||||||,-|ENSG00000085511|ENST00000544041|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MAP3K4|nonsense_mediated_decay|||||||,-|ENSG00000085511|ENST00000490904|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||MAP3K4|nonsense_mediated_decay|||||||,-|ENSG00000085511|ENST00000366920|Transcript|intron_variant&feature_truncation|||||MAP3K4|protein_coding|||||||,-|ENSG00000085511|ENST00000392142|Transcript|intron_variant&feature_truncation|||||MAP3K4|protein_coding|YES||||||,-||ENSR00001502269|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.38;PH=1.352;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.74,-104.1:6:99:54:8 1/0:-17.25,0,-45.55:5:99:48:15 6 162707838 . T C 2989 PASS Source=Platypus;CSQ=C|ENSG00000185345|ENST00000366897|Transcript|intron_variant|||||PARK2|protein_coding|||||||,C|ENSG00000185345|ENST00000479615|Transcript|intron_variant&NMD_transcript_variant|||||PARK2|nonsense_mediated_decay|||||||,C|ENSG00000185345|ENST00000366896|Transcript|intron_variant|||||PARK2|protein_coding|||||||,C|ENSG00000185345|ENST00000366898|Transcript|intron_variant|||||PARK2|protein_coding|YES||||||,C|ENSG00000185345|ENST00000338468|Transcript|intron_variant|||||PARK2|protein_coding|||||||,C|ENSG00000185345|ENST00000366894|Transcript|intron_variant|||||PARK2|protein_coding|||||||,C|ENSG00000185345|ENST00000366892|Transcript|intron_variant|||||PARK2|protein_coding|||||||;GR=1.95;PH=0.627;PS=0.003;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-17.1,-206.5:4:99:58:0 1/0:-69.95,0,-98.55:2:99:57:25 6 164886132 . T C 2728 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.451;PH=-0.759;PS=0.002;REPMASK=DNA;UK10K=1/7562 GT:GL:GOF:GQ:NR:NV 1/1:-169.7,-14.13,0:14:99:49:49 1/1:-180.5,-14.75,0:15:99:51:51 6 165455589 . TATT - 935 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.18;PH=-0.957;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-106.44,0,-100.64:1:99:59:30 1/0:-71.51,0,-60.01:0:99:44:25 6 168809140 . C T 99 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.322;PH=0.085;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-86.19,0,-78.19:2:99:61:32 1/0:-60.53,0,-83.03:3:99:54:23 7 1685300 . GC - 1637 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.66;PH=-1.124;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-164.2,-13.25,0:7:99:46:46 1/1:-177.2,-14.73,0:8:99:50:50 7 2414310 . C T 907 PASS Source=Platypus;CSQ=T|ENSG00000106263|ENST00000468611|Transcript|upstream_gene_variant||||1300|EIF3B|retained_intron|||||||,T|ENSG00000106263|ENST00000494658|Transcript|upstream_gene_variant||||4012|EIF3B|retained_intron|||||||,T|ENSG00000106263|ENST00000360876|Transcript|intron_variant|||||EIF3B|protein_coding|YES||||||,T|ENSG00000106263|ENST00000465670|Transcript|upstream_gene_variant||||3149|EIF3B|retained_intron|||||||,T|ENSG00000106263|ENST00000475415|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|1558||||EIF3B|retained_intron|||||||,T|ENSG00000106263|ENST00000466199|Transcript|downstream_gene_variant||||2485|EIF3B|retained_intron|||||||,T|ENSG00000106263|ENST00000397011|Transcript|intron_variant|||||EIF3B|protein_coding|||||||;GR=0.32;PH=0.069;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-80.29,0,-72.49:3:99:56:27 0/0:0,-11.98,-142.7:2:99:42:0 7 4143160 . T C 225 PASS Source=Platypus;CSQ=C|ENSG00000146555|ENST00000404826|Transcript|intron_variant|||||SDK1|protein_coding|YES||||||,C|ENSG00000146555|ENST00000389531|Transcript|intron_variant|||||SDK1|protein_coding|||||||,C||ENSR00001049121|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-3.88;PH=-0.79;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-11.95,-145.1:3:99:43:0 0/1:-64.7,0,-76.2:12:99:48:22 7 9010162 . A G 49 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=5.05;PH=2.111;PS=1 GT:GL:GOF:GQ:NR:NV 1/1:-176,-14.45,0:0:99:50:49 1/1:-159.1,-12.64,0:0:99:44:44 7 14496632 . A G 1713 PASS Source=Platypus;CSQ=G|ENSG00000136267|ENST00000403963|Transcript|intron_variant&non_coding_transcript_variant|||||DGKB|processed_transcript|||||||,G|ENSG00000136267|ENST00000258767|Transcript|intron_variant|||||DGKB|protein_coding|||||||,G|ENSG00000136267|ENST00000444700|Transcript|intron_variant|||||DGKB|protein_coding|||||||,G|ENSG00000136267|ENST00000403951|Transcript|intron_variant|||||DGKB|protein_coding|YES||||||,G|ENSG00000136267|ENST00000402815|Transcript|intron_variant|||||DGKB|protein_coding|||||||,G|ENSG00000136267|ENST00000407950|Transcript|intron_variant|||||DGKB|protein_coding|||||||,G|ENSG00000136267|ENST00000406247|Transcript|intron_variant|||||DGKB|protein_coding|||||||,G|ENSG00000136267|ENST00000399322|Transcript|intron_variant|||||DGKB|protein_coding|||||||;GR=0.258;PH=0.053;PS=0.09 GT:GL:GOF:GQ:NR:NV 0/1:-5.18,0,-79.98:22:52:16:1 0/1:-11.52,0,-56.68:40:99:15:2 7 16058235 . T C 1546 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.726;PH=-0.35;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.69,-226.2:3:99:65:0 1/0:-73.55,0,-71.35:0:99:51:27 7 17096492 . G A 1754 PASS Source=Platypus;CSQ=A||ENSR00001557586|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,A||||intergenic_variant|||||||||||||;GR=-1.71;PH=-0.339;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-1,-1,-1:6:16:28,28:4,4 0/2:-1,-1,-1:8:10:31,31:10,10 7 22497351 . G A 1802 PASS Source=Platypus;CSQ=A|ENSG00000105889|ENST00000404369|Transcript|intron_variant|||||STEAP1B|protein_coding|YES||||||,A|ENSG00000105889|ENST00000406890|Transcript|intron_variant|||||STEAP1B|protein_coding|||||||;GR=1.16;PH=0.126;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-83.35,0,-83.25:27:99:48:22 1/1:-181.4,-13.85,0:62:99:52:46 7 31150545 . A G 68 PASS Source=Platypus;CSQ=G|ENSG00000078549|ENST00000409363|Transcript|downstream_gene_variant||||3925|ADCYAP1R1|protein_coding|||||||,G|ENSG00000078549|ENST00000409489|Transcript|downstream_gene_variant||||4087|ADCYAP1R1|protein_coding|||||||,G|ENSG00000078549|ENST00000304166|Transcript|3_prime_UTR_variant|5943||||ADCYAP1R1|protein_coding|||||||,G|ENSG00000078549|ENST00000396211|Transcript|downstream_gene_variant||||4222|ADCYAP1R1|protein_coding|YES||||||;GR=-1.75;PH=-0.34;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.16,-206.2:1:99:59:0 0/1:-70.65,0,-80.85:1:99:52:25 7 34001085 . A G 1862 PASS Source=Platypus;CSQ=G|ENSG00000164619|ENST00000436222|Transcript|intron_variant|||||BMPER|protein_coding|||||||,G|ENSG00000164619|ENST00000444773|Transcript|intron_variant&NMD_transcript_variant|||||BMPER|nonsense_mediated_decay|||||||,G|ENSG00000164619|ENST00000297161|Transcript|intron_variant|||||BMPER|protein_coding|YES||||||,G|ENSG00000164619|ENST00000426693|Transcript|intron_variant|||||BMPER|protein_coding|||||||,G||ENSR00001558743|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.15;PH=0.302;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-6.92,-86.2:5:69:25:0 1/0:-63.66,0,-68.06:0:99:43:20 7 35084080 . C T 621 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.634;PH=-0.18;PS=0.005;REPMASK=Low_complexity;SD=0.970026 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.36,-221.3:1:99:63:0 1/0:-49.95,0,-102.75:0:99:50:18 7 35380963 . AA - 665 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.588;PH=-0.396;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-150.1,-12.34,0:2:99:43:43 1/1:-118.2,-9.42,0:4:94:33:33 7 36706517 . GTT - 1339 PASS Source=Platypus;CSQ=-|ENSG00000136250|ENST00000535891|Transcript|intron_variant&feature_truncation|||||AOAH|protein_coding|||||||,-|ENSG00000136250|ENST00000435386|Transcript|intron_variant&feature_truncation|||||AOAH|protein_coding|||||||,-|ENSG00000136250|ENST00000431169|Transcript|intron_variant&feature_truncation|||||AOAH|protein_coding|||||||,-|ENSG00000136250|ENST00000258749|Transcript|intron_variant&feature_truncation|||||AOAH|protein_coding|YES||||||;GR=0.109;PH=0.181;PS=0.086;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-50.4,-10.36,0:30:99:44:32 1/1:-43,-9.15,0:36:92:46:29 7 39454160 . G A 2972 PASS Source=Platypus;CSQ=A|ENSG00000106536|ENST00000520104|Transcript|intron_variant|||||POU6F2|protein_coding|||||||,A|ENSG00000106536|ENST00000403058|Transcript|intron_variant|||||POU6F2|protein_coding|YES||||||,A|ENSG00000106536|ENST00000559001|Transcript|intron_variant|||||POU6F2|protein_coding|||||||,A|ENSG00000106536|ENST00000524147|Transcript|intron_variant|||||POU6F2|protein_coding|||||||,A|ENSG00000106536|ENST00000416452|Transcript|intron_variant&NMD_transcript_variant|||||POU6F2|nonsense_mediated_decay|||||||,A|ENSG00000106536|ENST00000518318|Transcript|intron_variant|||||POU6F2|protein_coding|||||||,A||ENSR00000625018|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.56;PH=0.077;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-44.26,0,-21.26:24:99:54:24 1/0:-21.95,0,-41.85:29:99:50:16 7 47387017 . AA - 788 PASS Source=Platypus;CSQ=-|ENSG00000136205|ENST00000398879|Transcript|intron_variant&feature_truncation|||||TNS3|protein_coding|YES||||||,-|ENSG00000136205|ENST00000311160|Transcript|intron_variant&feature_truncation|||||TNS3|protein_coding|||||||,-|ENSG00000136205|ENST00000457718|Transcript|intron_variant&feature_truncation|||||TNS3|protein_coding|||||||,-|ENSG00000136205|ENST00000355730|Transcript|intron_variant&feature_truncation|||||TNS3|protein_coding|||||||;GR=0.751;PH=0.57;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-161.8,-8.73,0:3:87:29:28 1/1:-273.7,-14.45,0:1:99:47:43 7 48759258 . A G 2203 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-1.6;PH=-0.391;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.25,-144.5:2:99:41:0 1/1:-124.9,-10.54,0:2:99:36:36 7 52680675 . T C 2383 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.073;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-60.35,0,-80.55:8:99:53:25 1/1:-212.6,-17.76,0:5:99:61:60 7 57811873 . TCAC - 383 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.056;PS=0.032;REPMASK=Satellite;SD=0.963741 GT:GL:GOF:GQ:NR:NV 0/1:-110.33,0,-92.33:2:99:70:38 0/1:-97.24,0,-95.64:2:99:64:33 7 63977873 . C T 1998 PASS Source=Platypus;CSQ=T|ENSG00000173041|ENST00000309683|Transcript|downstream_gene_variant||||2389|ZNF680|protein_coding|YES||||||,T|ENSG00000173041|ENST00000470847|Transcript|downstream_gene_variant||||4955|ZNF680|retained_intron|||||||,T|ENSG00000173041|ENST00000476563|Transcript|downstream_gene_variant||||4431|ZNF680|processed_transcript|||||||;PH=0.119;PS=0.296;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-13.26,0,-30.16:7:99:48:12 0/0:0,-9.91,-54.4:2:99:40:0 7 78263031 . A G 1686 PASS Source=Platypus;CSQ=G|ENSG00000187391|ENST00000536571|Transcript|intron_variant|||||MAGI2|protein_coding|||||||,G|ENSG00000187391|ENST00000535697|Transcript|intron_variant|||||MAGI2|protein_coding|||||||,G|ENSG00000187391|ENST00000354212|Transcript|intron_variant|||||MAGI2|protein_coding|YES||||||,G|ENSG00000187391|ENST00000419488|Transcript|intron_variant|||||MAGI2|protein_coding|||||||,G|ENSG00000187391|ENST00000522391|Transcript|intron_variant|||||MAGI2|protein_coding|||||||;PH=0.139;PS=0.038;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-6.15,0,-47.95:10:61:32:6 0/1:-2.08,0,-41.18:8:21:21:7 7 80279578 . G A 1568 PASS Source=Platypus;CSQ=A|ENSG00000135218|ENST00000436384|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000538969|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000309881|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000544133|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000435819|Transcript|intron_variant|||||CD36|protein_coding|YES||||||,A|ENSG00000135218|ENST00000419819|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000432207|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000433696|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000480599|Transcript|downstream_gene_variant||||3047|CD36|retained_intron|||||||,A|ENSG00000135218|ENST00000534394|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000447544|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000441109|Transcript|intron_variant&non_coding_transcript_variant|||||CD36|processed_transcript|||||||,A|ENSG00000135218|ENST00000413265|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000526804|Transcript|downstream_gene_variant||||3536|CD36|processed_transcript|||||||,A|ENSG00000135218|ENST00000441034|Transcript|intron_variant&NMD_transcript_variant|||||CD36|nonsense_mediated_decay|||||||,A|ENSG00000135218|ENST00000426978|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000428497|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000482059|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000438020|Transcript|intron_variant|||||CD36|protein_coding|||||||,A|ENSG00000135218|ENST00000394788|Transcript|intron_variant|||||CD36|protein_coding|||||||;GR=-0.232;PH=-0.073;PS=0.012 GT:GL:GOF:GQ:NR:NV 1/1:-256.5,-20.77,0:20:99:69:69 0/1:-89.29,0,-131.69:8:99:64:26 7 82665664 . A G 2972 PASS Source=Platypus;CSQ=G|ENSG00000186472|ENST00000333891|Transcript|intron_variant|||||PCLO|protein_coding|YES||||||,G|ENSG00000186472|ENST00000423517|Transcript|intron_variant|||||PCLO|protein_coding|||||||,G|ENSG00000186472|ENST00000461143|Transcript|intron_variant&non_coding_transcript_variant|||||PCLO|processed_transcript|||||||;GR=0.38;PH=0.066;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-15.25,-177:2:99:53:0 1/0:-115.94,0,-54.94:2:99:61:38 7 83122057 . C T 1442 PASS Source=Platypus;CSQ=T|ENSG00000170381|ENST00000427262|Transcript|intron_variant|||||SEMA3E|protein_coding|||||||,T|ENSG00000170381|ENST00000453333|Transcript|intron_variant&NMD_transcript_variant|||||SEMA3E|nonsense_mediated_decay|||||||,T|ENSG00000170381|ENST00000307792|Transcript|intron_variant|||||SEMA3E|protein_coding|YES||||||,T|ENSG00000170381|ENST00000442159|Transcript|intron_variant|||||SEMA3E|protein_coding|||||||;PH=-1.495;PS=0.02;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 1/0:-77.85,0,-76.25:0:99:51:26 1/0:-62.65,0,-67.75:0:99:45:22 7 90126786 . GAGA - 1551 PASS Source=Platypus;CSQ=-|ENSG00000157224|ENST00000483862|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CLDN12|processed_transcript|||||||,-|ENSG00000157224|ENST00000498033|Transcript|downstream_gene_variant||||3056|CLDN12|processed_transcript|||||||,-|ENSG00000273299|ENST00000480135|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CTB-13L3.1|processed_transcript|YES||||||,-|ENSG00000157224|ENST00000485696|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CLDN12|processed_transcript|||||||,-|ENSG00000157224|ENST00000451941|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CLDN12|processed_transcript|||||||,-|ENSG00000058091|ENST00000449528|Transcript|intron_variant&feature_truncation|||||CDK14|protein_coding|||||||,-|ENSG00000157224|ENST00000476475|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CLDN12|processed_transcript|||||||;PH=0.064;PS=0.292;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-182.5:19:99:54:0 1/0:-92.86,0,-83.76:14:99:62:33 7 91498881 . C T 443 PASS Source=Platypus;CSQ=T|ENSG00000127989|ENST00000419292|Transcript|downstream_gene_variant||||1362|MTERF|protein_coding|||||||,T|ENSG00000127989|ENST00000456229|Transcript|downstream_gene_variant||||4748|MTERF|protein_coding|||||||,T|ENSG00000127989|ENST00000351870|Transcript|downstream_gene_variant||||3324|MTERF|protein_coding|YES||||||,T|ENSG00000127989|ENST00000406735|Transcript|downstream_gene_variant||||3755|MTERF|protein_coding|||||||,T|ENSG00000127989|ENST00000454222|Transcript|intron_variant&non_coding_transcript_variant|||||MTERF|processed_transcript|||||||,T|ENSG00000127989|ENST00000442961|Transcript|downstream_gene_variant||||4751|MTERF|protein_coding|||||||;GR=-1.28;PH=-0.254;PS=0.008 GT:GL:GOF:GQ:NR:NV 0/1:-61.65,0,-77.35:4:99:50:24 0/1:-97.69,0,-46.19:4:99:46:30 7 102626732 . T C 1163 PASS Source=Platypus;CSQ=C|ENSG00000161040|ENST00000379306|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000393772|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000456695|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000313221|Transcript|intron_variant|||||FBXL13|protein_coding|YES||||||,C|ENSG00000230257|ENST00000420058|Transcript|intron_variant&non_coding_transcript_variant|||||NFE4|antisense|YES||||||,C|ENSG00000161040|ENST00000455112|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000448002|Transcript|intron_variant&NMD_transcript_variant|||||FBXL13|nonsense_mediated_decay|||||||,C|ENSG00000161040|ENST00000379305|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000471074|Transcript|intron_variant&non_coding_transcript_variant|||||FBXL13|processed_transcript|||||||,C|ENSG00000161040|ENST00000436908|Transcript|intron_variant|||||FBXL13|protein_coding|||||||,C|ENSG00000161040|ENST00000379308|Transcript|intron_variant|||||FBXL13|protein_coding|||||||;GR=-2.8;PH=-0.736;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-77.25,0,-60.95:5:99:49:26 0/0:0,-16.26,-188.3:1:99:56:0 7 105531958 . G A 2826 PASS Source=Platypus;CSQ=A|ENSG00000128536|ENST00000488386|Transcript|intron_variant&NMD_transcript_variant|||||CDHR3|nonsense_mediated_decay|||||||,A|ENSG00000128536|ENST00000470188|Transcript|intron_variant&non_coding_transcript_variant|||||CDHR3|processed_transcript|||||||,A|ENSG00000128536|ENST00000487084|Transcript|intron_variant&non_coding_transcript_variant|||||CDHR3|processed_transcript|||||||,A|ENSG00000128536|ENST00000474330|Transcript|downstream_gene_variant||||1409|CDHR3|processed_transcript|||||||;GR=-6.03;PH=-1.404;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-61.38,0,-25.79:32:99:37:11 0/0:0,-5.77,-103.15:28:58:46:22 7 115000189 . A G 762 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.413;PH=-0.117;PS=0.014 GT:GL:GOF:GQ:NR:NV 1/1:-211.6,-17.16,0:8:99:60:59 1/1:-209.3,-16.56,0:9:99:58:58 7 116520040 . G A 1579 PASS Source=Platypus;CSQ=A|ENSG00000198898|ENST00000417431|Transcript|intron_variant&non_coding_transcript_variant|||||CAPZA2|processed_transcript|||||||,A|ENSG00000198898|ENST00000426421|Transcript|intron_variant&NMD_transcript_variant|||||CAPZA2|nonsense_mediated_decay|||||||,A|ENSG00000235945|ENST00000299783|Transcript|upstream_gene_variant||||3610|AC002543.2|processed_pseudogene|YES||||||,A|ENSG00000198898|ENST00000458284|Transcript|intron_variant|||||CAPZA2|protein_coding|||||||,A|ENSG00000198898|ENST00000464223|Transcript|intron_variant|||||CAPZA2|protein_coding|||||||,A|ENSG00000198898|ENST00000449080|Transcript|intron_variant&NMD_transcript_variant|||||CAPZA2|nonsense_mediated_decay|||||||,A|ENSG00000198898|ENST00000414148|Transcript|intron_variant&non_coding_transcript_variant|||||CAPZA2|processed_transcript|||||||,A|ENSG00000198898|ENST00000461878|Transcript|intron_variant&non_coding_transcript_variant|||||CAPZA2|retained_intron|||||||,A|ENSG00000198898|ENST00000484325|Transcript|intron_variant|||||CAPZA2|protein_coding|||||||,A|ENSG00000198898|ENST00000361183|Transcript|intron_variant|||||CAPZA2|protein_coding|YES||||||,A|ENSG00000198898|ENST00000490693|Transcript|intron_variant|||||CAPZA2|protein_coding|||||||,A|ENSG00000198898|ENST00000464669|Transcript|intron_variant&non_coding_transcript_variant|||||CAPZA2|retained_intron|||||||;GR=1.82;PH=1.557;PS=0.863;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-86.39,-5.76,0:12:58:23:18 1/1:-173.4,-12.28,0:5:99:42:36 7 121143942 . A G 1878 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.173;PH=0.026;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-126.35,0,-204.05:22:99:53:21 1/0:-108.15,0,-179.95:28:99:46:18 7 121993176 . C T 492 PASS Source=Platypus;CSQ=T|ENSG00000240499|ENST00000593910|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-1101C3.1|antisense|||||||,T|ENSG00000081803|ENST00000449022|Transcript|intron_variant|||||CADPS2|protein_coding|YES||||||,T|ENSG00000081803|ENST00000397721|Transcript|intron_variant|||||CADPS2|protein_coding|||||||,T|ENSG00000240499|ENST00000591140|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-1101C3.1|antisense|||||||,T|ENSG00000240499|ENST00000602199|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-1101C3.1|antisense|||||||,T|ENSG00000081803|ENST00000334010|Transcript|intron_variant|||||CADPS2|protein_coding|||||||,T|ENSG00000081803|ENST00000462699|Transcript|intron_variant|||||CADPS2|protein_coding|||||||,T|ENSG00000240499|ENST00000482375|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-1101C3.1|antisense|||||||,T|ENSG00000240499|ENST00000602012|Transcript|intron_variant&non_coding_transcript_variant|||||RP5-1101C3.1|antisense|YES||||||,T|ENSG00000081803|ENST00000313070|Transcript|intron_variant|||||CADPS2|protein_coding|||||||,T|ENSG00000081803|ENST00000412584|Transcript|intron_variant|||||CADPS2|protein_coding|||||||;GR=0.491;PH=0.162;PS=0;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-12,-135.9:2:99:43:0 0/1:-87.71,0,-56.21:1:99:53:32 7 124521741 . AAT - 2343 PASS Source=Platypus;CSQ=-|ENSG00000128513|ENST00000607932|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||POT1|nonsense_mediated_decay|||||||,-|ENSG00000128513|ENST00000446993|Transcript|intron_variant&feature_truncation|||||POT1|protein_coding|||||||,-|ENSG00000128513|ENST00000357628|Transcript|intron_variant&feature_truncation|||||POT1|protein_coding|YES||||||,-|ENSG00000128513|ENST00000609702|Transcript|intron_variant&feature_truncation|||||POT1|protein_coding|||||||,-|ENSG00000128513|ENST00000429326|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||POT1|nonsense_mediated_decay|||||||,-|ENSG00000128513|ENST00000609106|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||POT1|nonsense_mediated_decay|||||||,-|ENSG00000128513|ENST00000393329|Transcript|intron_variant&feature_truncation|||||POT1|protein_coding|||||||,-|ENSG00000128513|ENST00000608057|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||POT1|nonsense_mediated_decay|||||||;GR=-2.71;PH=-0.513;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-167,-15.55,0:2:99:54:53 1/0:-66.38,0,-82.48:3:99:50:23 7 125479157 . TC - 678 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.056;PS=0.035;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-140.1,-13.2,0:6:99:54:53 1/1:-147.8,-13.2,0:4:99:52:51 7 128399334 . G A 1184 PASS Source=Platypus;CSQ=A|ENSG00000128595|ENST00000449187|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000535623|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000479257|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000538546|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000542996|Transcript|intron_variant|||||CALU|protein_coding|YES||||||,A|ENSG00000244218|ENST00000493781|Transcript|upstream_gene_variant||||2057|RN7SL81P|misc_RNA|YES||||||,A|ENSG00000128595|ENST00000535011|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000493278|Transcript|intron_variant|||||CALU|protein_coding|||||||,A|ENSG00000128595|ENST00000249364|Transcript|intron_variant|||||CALU|protein_coding|||||||;GR=-4.42;PH=-0.66;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-201.2,-16.82,0:2:99:59:58 1/1:-222.3,-18.06,0:1:99:61:61 7 129291515 . A G 1911 PASS Source=Platypus;CSQ=G|ENSG00000106459|ENST00000353868|Transcript|intron_variant|||||NRF1|protein_coding|||||||,G|ENSG00000106459|ENST00000393232|Transcript|intron_variant|||||NRF1|protein_coding|YES||||||,G|ENSG00000106459|ENST00000393230|Transcript|intron_variant|||||NRF1|protein_coding|||||||,G|ENSG00000106459|ENST00000454688|Transcript|intron_variant|||||NRF1|protein_coding|||||||,G|ENSG00000106459|ENST00000539636|Transcript|intron_variant|||||NRF1|protein_coding|||||||,G|ENSG00000106459|ENST00000311967|Transcript|intron_variant|||||NRF1|protein_coding|||||||,G|ENSG00000106459|ENST00000223190|Transcript|intron_variant|||||NRF1|protein_coding|||||||;GR=3.37;PH=1.856;PS=0.999 GT:GL:GOF:GQ:NR:NV 0/0:0,-14.15,-172:2:99:52:0 1/0:-42.67,0,-47.57:3:99:33:16 7 130105665 . TT - 207 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.07;PH=0.739;PS=0.02;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-56.96,0,-62.36:3:99:43:20 0/1:-69.95,0,-80.15:0:99:50:24 7 131877467 . T C 1411 PASS Source=Platypus;CSQ=C|ENSG00000221866|ENST00000321063|Transcript|intron_variant|||||PLXNA4|protein_coding|||||||,C|ENSG00000221866|ENST00000359827|Transcript|intron_variant|||||PLXNA4|protein_coding|YES||||||;GR=-1.05;PH=-0.606;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-66.65,0,-64.95:11:99:45:22 0/0:0,-15.35,-189.2:2:99:52:0 7 135518494 . TT - 2035 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-1.63;PH=-0.276;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-44.23,0,-50.73:3:99:74:26 1/0:-44.05,0,-24.25:1:99:54:26 7 140020074 . T C 2261 PASS Source=Platypus;CSQ=C|ENSG00000157800|ENST00000477571|Transcript|intron_variant&NMD_transcript_variant|||||SLC37A3|nonsense_mediated_decay|||||||,C||ENSR00000314120|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1;PH=0.721;PS=0.236;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-11.29,0,-67.19:90:99:20:2 0/0:0,-6.75,-92.1:0:67:25:0 7 140709265 . TTCT - 537 PASS Source=Platypus;CSQ=-|ENSG00000090263|ENST00000485202|Transcript|downstream_gene_variant||||760|MRPS33|retained_intron|||||||,-|ENSG00000273081|ENST00000610021|Transcript|upstream_gene_variant||||4616|RP4-813F11.4|lincRNA|YES||||||,-|ENSG00000090263|ENST00000496958|Transcript|intron_variant&feature_truncation|||||MRPS33|protein_coding|||||||,-|ENSG00000090263|ENST00000324787|Transcript|intron_variant&feature_truncation|||||MRPS33|protein_coding|||||||,-|ENSG00000090263|ENST00000472343|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MRPS33|processed_transcript|||||||,-|ENSG00000090263|ENST00000496641|Transcript|downstream_gene_variant||||691|MRPS33|retained_intron|||||||,-|ENSG00000090263|ENST00000467334|Transcript|intron_variant&feature_truncation|||||MRPS33|protein_coding|||||||,-|ENSG00000090263|ENST00000484502|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||MRPS33|processed_transcript|||||||,-|ENSG00000090263|ENST00000469351|Transcript|intron_variant&feature_truncation|||||MRPS33|protein_coding|||||||,-|ENSG00000090263|ENST00000393008|Transcript|intron_variant&feature_truncation|||||MRPS33|protein_coding|YES||||||;GR=0.327;PH=0.065;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-76.41,0,-61.31:3:99:48:26 0/1:-85.49,0,-73.49:3:99:56:29 7 143657565 . A G 1798 PASS Source=Platypus;CSQ=G|ENSG00000243583|ENST00000466281|Transcript|downstream_gene_variant||||1363|RP4-669B10.3|lincRNA|YES||||||,G|ENSG00000213215|ENST00000392899|Transcript|missense_variant|539|168|M/V||OR2F1|protein_coding|YES|tolerated(0.07)|benign(0.001)||||,G|ENSG00000243583|ENST00000470988|Transcript|intron_variant&non_coding_transcript_variant|||||RP4-669B10.3|lincRNA|||||||;GR=1.72;PH=0.137;PS=0.12;SD=0.909933 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:85:99:62,61:51,28 1/2:-1,-1,-1:115:99:42,43:42,22 7 146398576 . TTGT - 1286 PASS Source=Platypus;CSQ=-|ENSG00000174469|ENST00000361727|Transcript|intron_variant&feature_truncation|||||CNTNAP2|protein_coding|YES||||||;GR=1.46;PH=0.164;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-31.59,-4.69,0:12:47:23:14 1/1:-51.9,-5.83,0:10:58:45:24 7 148442079 . T C 2446 PASS Source=Platypus;CSQ=C|ENSG00000055130|ENST00000602748|Transcript|intron_variant|||||CUL1|protein_coding|||||||,C|ENSG00000055130|ENST00000325222|Transcript|intron_variant|||||CUL1|protein_coding|YES||||||,C|ENSG00000055130|ENST00000409469|Transcript|intron_variant|||||CUL1|protein_coding|||||||;GR=0.982;PH=0.685;PS=0.019;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-18.36,-218.1:2:99:63:0 1/0:-91.75,0,-74.05:3:99:57:31 7 150847528 . AT - 306 PASS Source=Platypus;CSQ=-|ENSG00000164900|ENST00000475831|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||GBX1|processed_transcript|||||||,-|ENSG00000164900|ENST00000297537|Transcript|intron_variant&feature_truncation|||||GBX1|protein_coding|YES||||||;GR=-3.24;PH=-0.9;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.5,-159.1:26:99:49:0 0/1:-54.16,0,-60.56:13:99:40:19 7 152059353 . A G 630 PASS Source=Platypus;CSQ=G|ENSG00000055609|ENST00000452749|Transcript|intron_variant|||||KMT2C|protein_coding|||||||,G|ENSG00000204894|ENST00000472406|Transcript|upstream_gene_variant||||4903|RP11-208G20.2|processed_pseudogene|YES||||||,G|ENSG00000055609|ENST00000355193|Transcript|intron_variant|||||KMT2C|protein_coding|||||||,G|ENSG00000270405|ENST00000603054|Transcript|upstream_gene_variant||||4495|RP11-208G20.3|processed_pseudogene|YES||||||,G|ENSG00000055609|ENST00000262189|Transcript|intron_variant|||||KMT2C|protein_coding|YES||||||,G|ENSG00000055609|ENST00000558084|Transcript|intron_variant&NMD_transcript_variant|||||KMT2C|nonsense_mediated_decay|||||||,G||ENSR00000314863|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.17;PH=0.77;PS=0.008;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-110.74,0,-55.34:3:99:55:35 0/1:-90.46,0,-74.26:4:99:54:29 7 153168037 . TA - 1930 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-3.48;PH=-2.028;PS=0;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-67.55,0,-125.95:3:99:71:27 0/0:0,-17.76,-218.6:7:99:61:0 7 157709748 . ACCA - 301 PASS Source=Platypus;CSQ=-|ENSG00000155093|ENST00000409483|Transcript|intron_variant&feature_truncation|||||PTPRN2|protein_coding|||||||,-|ENSG00000155093|ENST00000389416|Transcript|intron_variant&feature_truncation|||||PTPRN2|protein_coding|||||||,-|ENSG00000155093|ENST00000404321|Transcript|intron_variant&feature_truncation|||||PTPRN2|protein_coding|||||||,-|ENSG00000155093|ENST00000389418|Transcript|intron_variant&feature_truncation|||||PTPRN2|protein_coding|YES||||||,-|ENSG00000155093|ENST00000389413|Transcript|intron_variant&feature_truncation|||||PTPRN2|protein_coding|||||||;GR=-1.13;PH=-2.635;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.55,-166.1:3:99:48:0 1/1:-183.9,-14.75,0:42:99:49:49 8 2260613 . AGA - 2618 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.351;PH=0.338;PS=0.009;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-83.1,-6.59,0:1:66:23:23 1/1:-77.7,-6.02,0:0:60:21:21 8 5003026 . TC - 845 PASS Source=Platypus;CSQ=-|ENSG00000242079|ENST00000471955|Transcript|upstream_gene_variant||||2797|RN7SL318P|misc_RNA|YES||||||;GR=1.71;PH=0.378;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-103.21,0,-65.31:2:99:58:35 0/0:0,-14.75,-178:1:99:52:0 8 15672085 . G A 284 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-5.83;PH=-1.048;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-59.15,0,-63.25:27:99:47:22 0/0:0,-13.55,-163.6:11:99:46:0 8 16088808 . A G 2366 PASS Source=Platypus;CSQ=G|ENSG00000038945|ENST00000518026|Transcript|intron_variant|||||MSR1|protein_coding|||||||,G||ENSR00001386531|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.494;PH=0.122;PS=0.007;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/1:-10.39,0,-12.29:14:99:36:12 0/0:0,-2.33,-25.3:17:23:33:6 8 17359538 . TT - 2042 PASS Source=Platypus;CSQ=-|ENSG00000003989|ENST00000522656|Transcript|intron_variant&feature_truncation|||||SLC7A2|protein_coding|||||||,-|ENSG00000003989|ENST00000494857|Transcript|intron_variant&feature_truncation|||||SLC7A2|protein_coding|||||||,-|ENSG00000003989|ENST00000470360|Transcript|intron_variant&feature_truncation|||||SLC7A2|protein_coding|||||||;GR=-2.51;PH=-0.507;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.78,-196.9:2:99:58:1 0/1:-79.19,0,-59.89:1:99:48:27 8 23057155 . G A 2886 PASS Source=Platypus;CSQ=A|ENSG00000104689|ENST00000221132|Transcript|intron_variant|||||TNFRSF10A|protein_coding|YES||||||,A|ENSG00000104689|ENST00000519862|Transcript|upstream_gene_variant||||2369|TNFRSF10A|retained_intron|||||||,A|ENSG00000104689|ENST00000524158|Transcript|downstream_gene_variant||||244|TNFRSF10A|protein_coding|||||||;GR=-2.16;PH=-0.548;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-74.85,0,-68.85:3:99:49:25 1/0:-99.04,0,-73.84:0:99:57:32 8 26341540 . G A 1549 PASS Source=Platypus;CSQ=A|ENSG00000104765|ENST00000523949|Transcript|intron_variant|||||BNIP3L|protein_coding|||||||;GR=1.9;PH=0.509;PS=0.868 GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:6:48:31,31:9,9 1/2:-1,-1,-1:5:77:28,28:13,13 8 30236774 . A G 2377 PASS Source=Platypus;CSQ=G|ENSG00000254109|ENST00000519753|Transcript|downstream_gene_variant||||2866|RBPMS-AS1|antisense|YES||||||,G|ENSG00000254109|ENST00000523643|Transcript|downstream_gene_variant||||2866|RBPMS-AS1|antisense|||||||,G|ENSG00000254109|ENST00000517521|Transcript|downstream_gene_variant||||2861|RBPMS-AS1|antisense|||||||;GR=0.637;PH=0.495;PS=0.03;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-81.78,0,-80.78:3:99:59:31 0/0:0,-16.56,-201.2:16:99:56:0 8 34432272 . GA - 1380 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-5.38;PH=-1.371;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-275.2,-57.71,0:1:99:46:39 1/0:-142.73,0,-154.33:1:99:58:21 8 36971753 . AC - 961 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.017;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/0:-14.71,0,-33.01:39:99:22:8 0/0:0,-5.12,-58.9:11:51:25:1 8 40266445 . TTCC - 2792 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.95;PH=0.132;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-192.5,-16.23,0:3:99:56:56 1/1:-174.9,-14.24,0:2:99:50:50 8 43081127 . C T 2503 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.0465;PH=0.132;PS=0.41;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-94.9,-8.58,0:3:86:33:33 0/0:0,-6.51,-58.5:68:65:26:0 8 53757378 . C T 1054 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.15;PH=0.448;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-89.37,0,-88.07:1:99:62:31 0/0:0,-17.76,-218.7:0:99:60:0 8 57825400 . C T 976 PASS Source=Platypus;CSQ=T|ENSG00000206975|ENST00000384248|Transcript|upstream_gene_variant||||4243|RNU6-13P|snRNA|YES||||||;GR=0.49;PH=0.149;PS=0.001;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-14.45,-174.6:3:99:51:0 1/0:-64.75,0,-84.15:3:99:52:23 8 69134010 . A G 1939 PASS Source=Platypus;CSQ=G|ENSG00000252210|ENST00000516401|Transcript|downstream_gene_variant||||1543|Y_RNA|misc_RNA|YES||||||,G|ENSG00000046889|ENST00000288368|Transcript|intron_variant|||||PREX2|protein_coding|YES||||||,G|ENSG00000046889|ENST00000520235|Transcript|downstream_gene_variant||||1425|PREX2|processed_transcript|||||||;GR=-0.924;PH=-0.16;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-56.75,0,-73.75:5:99:47:22 0/0:0,-16.2,-196.7:1:99:56:0 8 70815987 . T C 1034 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;PH=0.103;PS=0.223;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-253.1,-20.47,0:1:99:71:71 1/0:-64.45,0,-79.75:2:99:46:21 8 71935590 . TG - 1489 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.109;PH=0.156;PS=0.14;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-6.12,0,-23.06:63:61:30:9 0/0:0,-8.8,-36.06:61:88:33:8 8 72552444 . A G 1056 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.149;PH=0.166;PS=0.09;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-66.83,0,-127.33:2:99:67:26 0/0:0,-21.37,-261.4:2:99:72:0 8 74908025 . AA - 2224 PASS Source=Platypus;CSQ=-|ENSG00000154589|ENST00000284818|Transcript|intron_variant&feature_truncation|||||LY96|protein_coding|YES||||||,-|ENSG00000154589|ENST00000518893|Transcript|intron_variant&feature_truncation|||||LY96|protein_coding|||||||;GR=1.6;PH=0.985;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-11.63,-143.3:1:99:41:0 1/0:-57.48,0,-90.68:0:99:48:20 8 78133725 . T C 402 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.993;PH=0.27;PS=0;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-86.76,0,-100.36:2:99:62:29 0/0:0,-14.45,-184.8:0:99:50:0 8 81780152 . TT - 833 PASS Source=Platypus;CSQ=-|ENSG00000164684|ENST00000519936|Transcript|intron_variant&feature_truncation|||||ZNF704|protein_coding|||||||,-|ENSG00000164684|ENST00000327835|Transcript|intron_variant&feature_truncation|||||ZNF704|protein_coding|YES||||||,-||ENSR00001442569|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=4.1;PH=2.092;PS=0.973 GT:GL:GOF:GQ:NR:NV 1/1:-231.8,-19.87,0:1:99:67:67 1/1:-210.4,-17.46,0:2:99:61:61 8 83015325 . A G 1284 PASS Source=Platypus;CSQ=G|ENSG00000254123|ENST00000520155|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-99H20.1|lincRNA|YES||||||;GR=1.76;PH=1.08;PS=0.145;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-122.43,0,-80.03:1:99:67:38 0/0:0,-15.65,-185.7:3:99:55:0 8 85443782 . A G 608 PASS Source=Platypus;CSQ=G|ENSG00000184672|ENST00000522647|Transcript|downstream_gene_variant||||2083|RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000521268|Transcript|intron_variant|||||RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000522455|Transcript|intron_variant|||||RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000517638|Transcript|intron_variant|||||RALYL|protein_coding|YES||||||,G|ENSG00000184672|ENST00000517988|Transcript|intron_variant|||||RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000521695|Transcript|intron_variant|||||RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000522613|Transcript|downstream_gene_variant||||1970|RALYL|protein_coding|||||||,G|ENSG00000184672|ENST00000518566|Transcript|intron_variant|||||RALYL|protein_coding|||||||;GR=2.22;PH=0.677;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-18.96,-225.3:3:99:66:0 0/1:-112.57,0,-80.27:1:99:70:38 8 99225771 . AT - 549 PASS Source=Platypus;CSQ=-|ENSG00000104361|ENST00000520735|Transcript|downstream_gene_variant||||3659|NIPAL2|processed_transcript|||||||,-|ENSG00000104361|ENST00000520545|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NIPAL2|processed_transcript|||||||,-|ENSG00000104361|ENST00000430223|Transcript|intron_variant&feature_truncation|||||NIPAL2|protein_coding|||||||,-|ENSG00000104361|ENST00000522188|Transcript|downstream_gene_variant||||3481|NIPAL2|processed_transcript|||||||,-|ENSG00000104361|ENST00000341166|Transcript|intron_variant&feature_truncation|||||NIPAL2|protein_coding|YES||||||,-||ENSR00001443436|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=2.72;PH=1.477;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-62.85,0,-76.45:1:99:50:23 1/1:-204.8,-16.23,0:0:99:57:57 8 105610621 . T C 671 PASS Source=Platypus;CSQ=C|ENSG00000253350|ENST00000521923|Transcript|intron_variant|||||RP11-127H5.1|protein_coding|YES||||||;GR=1.56;PH=0.472;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-102.4,-6.62,0:6:66:34:16 1/1:-139.3,-9.14,0:5:91:43:26 8 108376307 . T C 1502 PASS Source=Platypus;CSQ=C|ENSG00000154188|ENST00000520033|Transcript|intron_variant|||||ANGPT1|protein_coding|||||||,C|ENSG00000154188|ENST00000517746|Transcript|intron_variant|||||ANGPT1|protein_coding|YES||||||,C|ENSG00000154188|ENST00000297450|Transcript|intron_variant|||||ANGPT1|protein_coding|||||||;GR=-0.386;PH=-0.08;PS=0.006 GT:GL:GOF:GQ:NR:NV 1/0:-71.76,0,-52.26:3:99:42:23 0/0:0,-14.07,-170.1:10:99:49:0 8 112138118 . AC - 875 PASS Source=Platypus;CSQ=-|ENSG00000253103|ENST00000519506|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-946L20.4|lincRNA|||||||;GR=1.11;PH=0.784;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/1:-72.66,0,-68.16:1:99:58:14 0/1:-107.55,0,-77.65:3:99:68:18 8 114887307 . TT - 390 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.35;PH=0.387;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-220.7,-17.74,0:2:99:62:62 1/1:-177.9,-13.85,0:2:99:48:48 8 116839709 . TA - 2044 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.225;PH=0.257;PS=0.021;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-66.86,0,-59.46:0:99:41:21 1/1:-182.7,-15.03,0:0:99:51:51 8 119887167 . GAA - 130 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.5;PH=0.652;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/1:-194.6,-15.95,0:2:99:54:54 1/0:-100.24,0,-93.94:0:99:63:33 8 120003524 . TCCC - 813 PASS Source=Platypus;CSQ=-|ENSG00000184374|ENST00000521788|Transcript|upstream_gene_variant||||4164|COLEC10|processed_transcript|||||||;GR=1.2;PH=0.24;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-3.31,-43.6:0:33:13:0 1/1:-11.4,-0.6,0:9:7:4:3 8 120445593 . TACA - 490 PASS Source=Platypus;CSQ=-|ENSG00000253398|ENST00000519786|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-775B15.2|antisense|YES||||||;GR=0.174;PH=0.025;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/1:-172.4,-57.5,0:2:99:51:51 0/0:0,-10.53,-133.7:1:99:36:0 8 122884317 . T C 2673 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=1.39;PH=0.924;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-220.4,-18.36,0:3:99:64:64 1/1:-210.7,-17.09,0:4:99:63:63 8 130405891 . A G 1797 PASS Source=Platypus;CSQ=G|ENSG00000229140|ENST00000446592|Transcript|intron_variant&non_coding_transcript_variant|||||CCDC26|lincRNA|YES||||||,G|ENSG00000229140|ENST00000520048|Transcript|intron_variant&non_coding_transcript_variant|||||CCDC26|lincRNA|||||||,G|ENSG00000229140|ENST00000523151|Transcript|intron_variant&non_coding_transcript_variant|||||CCDC26|lincRNA|||||||;GR=2.01;PH=1.167;PS=0.104 GT:GL:GOF:GQ:NR:NV 1/1:-186.3,-15.59,0:2:99:54:54 1/1:-196.2,-15.65,0:1:99:53:53 8 131919844 . CA - 1782 PASS Source=Platypus;CSQ=-|ENSG00000155897|ENST00000286355|Transcript|intron_variant&feature_truncation|||||ADCY8|protein_coding|YES||||||,-|ENSG00000155897|ENST00000522949|Transcript|intron_variant&feature_truncation|||||ADCY8|protein_coding|||||||,-|ENSG00000155897|ENST00000377928|Transcript|intron_variant&feature_truncation|||||ADCY8|protein_coding|||||||,-||ENSR00001445723|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.235;PH=0.308;PS=0.087;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-15.35,-186:1:99:53:0 1/1:-168.3,-13.25,0:0:99:46:46 8 135840364 . G A 2218 PASS Source=Platypus;CSQ=A|ENSG00000254028|ENST00000521444|Transcript|upstream_gene_variant||||4626|AC083843.2|lincRNA|YES||||||;GR=1.19;PH=0.15;PS=0.028 GT:GL:GOF:GQ:NR:NV 0/0:0,-19.87,-243.6:7:99:68:0 0/1:-96.74,0,-83.74:1:99:60:31 8 136093454 . C T 2594 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=2.07;PH=0.6;PS=0.871 GT:GL:GOF:GQ:NR:NV 1/1:-212.2,-17.76,0:2:99:60:60 1/1:-217.8,-17.74,0:2:99:59:59 8 136798086 . G A 1302 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.109;PH=0.181;PS=0.093;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-79.14,0,-87.24:11:99:58:28 0/1:-61.85,0,-77.65:7:99:46:20 8 137082834 . G A 675 PASS Source=Platypus;CSQ=A|ENSG00000253248|ENST00000523150|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-149P24.1|lincRNA|YES||||||,A|ENSG00000253248|ENST00000502901|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-149P24.1|lincRNA|||||||;GR=2.17;PH=1.541;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-198.6,-16.54,0:1:99:57:57 1/1:-201.5,-15.95,0:0:99:54:54 8 138287254 . A G 1780 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=2.42;PH=0.418;PS=0.053 GT:GL:GOF:GQ:NR:NV 1/1:-185,-15.05,0:1:99:54:54 1/1:-151.8,-12.34,0:0:99:43:43 8 139982183 . T C 1401 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.743;PH=0.582;PS=0.038 GT:GL:GOF:GQ:NR:NV 1/0:-80.98,0,-89.78:3:99:57:26 0/0:0,-70.59,-169.3:3:99:54:1 8 140037826 . ACAT - 760 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=-0.696;PH=-0.387;PS=0.002;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-78.75,0,-76.25:2:99:51:27 0/1:-87.55,0,-75.95:0:99:54:29 8 142649239 . G A 491 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.945;PH=0.513;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-20.66,0,-299.7:11:99:80:7 1/0:-26.9,0,-299.7:7:99:67:6 8 144881568 . CC - 1300 PASS Source=Platypus;CSQ=-|ENSG00000180900|ENST00000377533|Transcript|intron_variant&feature_truncation|||||SCRIB|protein_coding|||||||,-|ENSG00000180900|ENST00000526832|Transcript|intron_variant&feature_truncation|||||SCRIB|protein_coding|||||||,-|ENSG00000180900|ENST00000356994|Transcript|intron_variant&feature_truncation|||||SCRIB|protein_coding|YES||||||,-|ENSG00000180900|ENST00000320476|Transcript|intron_variant&feature_truncation|||||SCRIB|protein_coding|||||||;GR=-1.59;PH=-1.954;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-66.39,0,-96.69:48:99:62:26 0/0:0,-11.44,-140.1:1:99:41:0 9 2553419 . A G 1542 PASS Source=Platypus;CSQ=G|ENSG00000236404|ENST00000416826|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-125B21.2|antisense|YES||||||,G|ENSG00000236404|ENST00000453601|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-125B21.2|antisense|||||||,G|ENSG00000236404|ENST00000424605|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-125B21.2|antisense|||||||;GR=-4.03;PH=-1.112;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-20.94,0,-159.24:4:99:62:12 1/0:-2,0,-190.3:3:20:65:6 9 7222937 . T C 2408 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.979;PH=0.208;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/0:0,-17.16,-210.3:3:99:59:0 0/1:-89.18,0,-37.98:6:99:45:30 9 9540080 . GA - 1417 PASS Source=Platypus;CSQ=-|ENSG00000153707|ENST00000463477|Transcript|intron_variant&feature_truncation|||||PTPRD|protein_coding|||||||,-|ENSG00000153707|ENST00000381196|Transcript|intron_variant&feature_truncation|||||PTPRD|protein_coding|YES||||||;GR=-6.81;PH=-2.129;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-51.28,0,-18.38:5:99:30:18 1/0:-63.29,0,-74.39:4:99:58:27 9 12032314 . T C 1747 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-1.4;PH=-0.109;PS=0.01 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.57,-146.7:6:99:44:0 1/0:-48.23,0,-52.33:0:99:38:19 9 12426821 . A G 2088 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=0.158;PH=0.175;PS=0.008;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-97.7,-7.26,0:17:73:29:28 1/1:-167.5,-13.75,0:1:99:46:46 9 14425156 . C T 2335 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=-0.801;PH=-0.181;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-83.54,0,-69.84:3:99:55:30 1/1:-151,-13.25,0:2:99:46:46 9 24771490 . C T 2031 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.21;PH=0.988;PS=0.001;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-36.46,0,-82.16:5:99:42:15 1/0:-65.2,0,-49.2:5:99:44:25 9 27918450 . TC - 804 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.23;PH=0.062;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-93.65,0,-61.75:1:99:52:30 1/0:-80.74,0,-95.54:0:99:58:28 9 31954103 . CTTT - 1227 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.119;PS=0.202;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-6.6,-0.79,0:34:9:6:4 1/0:-7.6,0,-3.9:45:39:6:4 9 71043265 . CAAT - 551 PASS Source=Platypus;CSQ=-|ENSG00000154330|ENST00000396392|Transcript|intron_variant&feature_truncation|||||PGM5|protein_coding|||||||,-|ENSG00000229019|ENST00000434656|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-88I18.3|sense_intronic|YES||||||,-|ENSG00000154330|ENST00000396396|Transcript|intron_variant&feature_truncation|||||PGM5|protein_coding|YES||||||;GR=-0.59;PH=-0.211;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-210.5,-15.95,0:2:99:55:49 1/1:-155.4,-11.74,0:3:99:43:38 9 71706587 . T C 1553 PASS Source=Platypus;CSQ=C|ENSG00000165060|ENST00000396364|Transcript|intron_variant|||||FXN|protein_coding|||||||;GR=-0.639;PH=-0.319;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-77.05,0,-86.55:1:99:54:26 0/0:0,-14.15,-180.5:2:99:49:0 9 72284481 . ATTT - 2288 PASS Source=Platypus;CSQ=-|ENSG00000261447|ENST00000567129|Transcript|upstream_gene_variant||||3181|RP11-109D9.4|lincRNA|YES||||||,-|ENSG00000107282|ENST00000265381|Transcript|intron_variant&feature_truncation|||||APBA1|protein_coding|YES||||||;GR=1.53;PH=0.222;PS=0.117 GT:GL:GOF:GQ:NR:NV 0/2:-1,-1,-1:5:99:52,52:16,16 1/0:-1,-1,-1:13:99:47,47:23,23 9 78236140 . TG - 2485 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.109;PH=0.156;PS=0.3;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-169.42,0,-138.72:23:99:109:60 1/0:-38.64,0,-201.54:20:99:86:18 9 82841874 . TT - 136 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.103;PS=0.455;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-12.18,-144.8:6:99:46:0 0/1:-55.89,0,-76.29:7:99:48:20 9 88202498 . ATTA - 1595 PASS Source=Platypus;CSQ=-|ENSG00000135049|ENST00000357081|Transcript|intron_variant&feature_truncation|||||AGTPBP1|protein_coding|||||||,-|ENSG00000135049|ENST00000376083|Transcript|intron_variant&feature_truncation|||||AGTPBP1|protein_coding|YES||||||,-|ENSG00000135049|ENST00000337006|Transcript|intron_variant&feature_truncation|||||AGTPBP1|protein_coding|||||||,-|ENSG00000135049|ENST00000376109|Transcript|intron_variant&feature_truncation|||||AGTPBP1|protein_coding|||||||,-|ENSG00000135049|ENST00000432218|Transcript|intron_variant&feature_truncation|||||AGTPBP1|protein_coding|||||||;GR=3.98;PH=1.656;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/1:-167.1,-13.25,0:15:99:44:44 1/1:-230,-18.34,0:6:99:61:61 9 89995488 . T C 2787 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.912;PH=0.2;PS=0.111 GT:GL:GOF:GQ:NR:NV 0/1:-88.83,0,-113.73:8:99:70:31 1/1:-183,-14.75,0:9:99:50:50 9 93037440 . T C 79 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.565;PH=0.47;PS=0.005;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 0/0:0,-13.51,-158:1:99:48:0 1/0:-90.65,0,-51.15:1:99:51:30 9 93341998 . GC - 2052 PASS Source=Platypus;CSQ=-|ENSG00000229613|ENST00000449990|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-555F9.2|lincRNA|YES||||||,-|ENSG00000229613|ENST00000429044|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||RP11-555F9.2|lincRNA|||||||;GR=-2.1;PH=-0.564;PS=0 GT:GL:GOF:GQ:NR:NV 1/1:-130.5,-11.66,0:28:99:42:42 0/1:-72.08,0,-57.08:14:99:44:24 9 95085805 . ACAA - 311 PASS Source=Platypus;CSQ=-|ENSG00000198000|ENST00000538215|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NOL8|processed_transcript|||||||,-|ENSG00000198000|ENST00000543985|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NOL8|processed_transcript|||||||,-|ENSG00000198000|ENST00000542613|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000545558|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|YES||||||,-|ENSG00000198000|ENST00000360868|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000542573|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000433029|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000543260|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000544321|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000358855|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000442668|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000535387|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000411621|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000545444|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000544867|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000536593|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000542053|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000445919|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000535649|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NOL8|retained_intron|||||||,-|ENSG00000198000|ENST00000432670|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000467230|Transcript|upstream_gene_variant||||4576|NOL8|retained_intron|||||||,-|ENSG00000198000|ENST00000536624|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000434228|Transcript|intron_variant&NMD_transcript_variant&feature_truncation|||||NOL8|nonsense_mediated_decay|||||||,-|ENSG00000198000|ENST00000421075|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000198000|ENST00000535807|Transcript|intron_variant&feature_truncation|||||NOL8|protein_coding|||||||,-|ENSG00000188312|ENST00000375587|Transcript|upstream_gene_variant||||1958|CENPP|protein_coding|YES||||||,-|ENSG00000198000|ENST00000482475|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||NOL8|retained_intron|||||||;GR=0.559;PH=0.469;PS=0.001;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/0:0,-17.41,-202:2:99:61:0 0/1:-81.92,0,-47.82:10:99:43:26 9 98602663 . T C 681 PASS Source=Platypus;CSQ=C|ENSG00000175611|ENST00000429781|Transcript|downstream_gene_variant||||219|LINC00476|processed_transcript|YES||||||,C|ENSG00000175611|ENST00000412446|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00476|processed_transcript|||||||,C|ENSG00000175611|ENST00000433656|Transcript|intron_variant&non_coding_transcript_variant|||||LINC00476|processed_transcript|||||||;GR=-2.57;PH=-0.556;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-55.01,0,-85.91:10:99:52:21 0/0:0,-12.15,-178.8:2:99:52:1 9 102105896 . C T 1671 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.38;PH=1.07;PS=0.007 GT:GL:GOF:GQ:NR:NV 1/0:-71.5,0,-68.8:35:99:48:25 0/0:0,-14.11,-177.8:17:99:49:0 9 110667007 . TGA - 1145 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.564;PH=0.116;PS=0.003 GT:GL:GOF:GQ:NR:NV 1/0:-103.63,0,-88.63:0:99:65:35 0/0:0,-18.58,-223.9:3:99:64:0 9 111998299 . A G 2916 PASS Source=Platypus;CSQ=G|ENSG00000095203|ENST00000374566|Transcript|intron_variant|||||EPB41L4B|protein_coding|YES||||||,G|ENSG00000095203|ENST00000374557|Transcript|downstream_gene_variant||||3712|EPB41L4B|protein_coding|||||||;GR=-4.72;PH=-0.874;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-88.2,0,-55.8:6:99:51:29 0/1:-76.28,0,-63.28:4:99:49:26 9 116031245 . GGA - 41 PASS Source=Platypus;CSQ=-|ENSG00000136868|ENST00000374212|Transcript|downstream_gene_variant||||4473|SLC31A1|protein_coding|YES||||||,-|ENSG00000176386|ENST00000374206|Transcript|intron_variant&feature_truncation|||||CDC26|protein_coding|YES||||||,-|ENSG00000176386|ENST00000490408|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||CDC26|processed_transcript|||||||,-|ENSG00000136868|ENST00000374210|Transcript|downstream_gene_variant||||2571|SLC31A1|protein_coding|||||||;GR=0.336;PH=0.385;PS=0.002;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-9.55,0,-67.53:24:96:37:31 1/0:-1.08,0,-82.7:17:11:33:18 9 116762626 . A G 1886 PASS Source=Platypus;CSQ=G|ENSG00000157657|ENST00000452710|Transcript|intron_variant|||||ZNF618|protein_coding|||||||,G|ENSG00000157657|ENST00000288466|Transcript|intron_variant|||||ZNF618|protein_coding|YES||||||,G|ENSG00000157657|ENST00000481558|Transcript|intron_variant&non_coding_transcript_variant|||||ZNF618|processed_transcript|||||||,G|ENSG00000157657|ENST00000374124|Transcript|intron_variant|||||ZNF618|protein_coding|||||||,G|ENSG00000157657|ENST00000374126|Transcript|intron_variant|||||ZNF618|protein_coding|||||||;PH=0.106;PS=0.02;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-92.04,0,-47.04:1:99:52:33 0/0:0,-15.65,-193:0:99:53:0 9 123411823 . G A 2291 PASS Source=Platypus;CSQ=A|ENSG00000106780|ENST00000426959|Transcript|intron_variant|||||MEGF9|protein_coding|||||||,A|ENSG00000106780|ENST00000373930|Transcript|intron_variant|||||MEGF9|protein_coding|YES||||||;GR=0.596;PH=0.636;PS=0.02;REPMASK=DNA GT:GL:GOF:GQ:NR:NV 1/1:-204.5,-17.4,0:2:99:62:62 1/1:-222.7,-17.76,0:2:99:61:61 9 123994097 . C T 1922 PASS Source=Platypus;CSQ=T|ENSG00000148180|ENST00000373823|Transcript|intron_variant|||||GSN|protein_coding|||||||,T|ENSG00000148180|ENST00000434663|Transcript|intron_variant&non_coding_transcript_variant|||||GSN|processed_transcript|||||||;GR=0.69;PH=0.634;PS=0.079;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-160.3,-13.81,0:4:99:49:49 0/0:0,-14.15,-181.3:13:99:49:0 9 125486130 . G A 1693 PASS Source=Platypus;CSQ=A|ENSG00000136939|ENST00000259466|Transcript|upstream_gene_variant||||139|OR1L4|protein_coding|YES||||||;GR=-9.74;PH=-3.844;PS=0 GT:GL:GOF:GQ:NR:NV 0/1:-54.67,0,-89.07:3:99:56:25 0/1:-45.62,0,-71.52:1:99:42:18 9 129298121 . T C 2134 PASS Source=Platypus;CSQ=C|ENSG00000221768|ENST00000408841|Transcript|upstream_gene_variant||||4851|AL356309.1|miRNA|YES||||||;GR=-1.35;PH=-1.367;PS=0;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-28.75,0,-30.25:6:99:54:17 1/0:-20.84,0,-27.74:2:99:45:15 9 136844992 . T C 36 PASS Source=Platypus;CSQ=C|ENSG00000160293|ENST00000371850|Transcript|intron_variant|||||VAV2|protein_coding|YES||||||,C|ENSG00000160293|ENST00000486113|Transcript|intron_variant&non_coding_transcript_variant|||||VAV2|processed_transcript|||||||,C|ENSG00000160293|ENST00000406606|Transcript|intron_variant|||||VAV2|protein_coding|||||||,C|ENSG00000160293|ENST00000371851|Transcript|intron_variant|||||VAV2|protein_coding|||||||,C||ENSR00001316897|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-5.13;PH=-1.773;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-19.53,-238.5:1:99:66:1 1/0:-60.24,0,-113.04:1:99:61:25 9 136948132 . TA - 328 PASS Source=Platypus;CSQ=-|ENSG00000271525|ENST00000605447|Transcript|downstream_gene_variant||||3566|RP11-349K21.1|processed_pseudogene|YES||||||;PH=0.356;PS=0.33;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-12.32,0,-25.42:7:99:57:18 0/1:-7.99,0,-17.89:8:80:39:14 9 137391681 . G A 1236 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;PH=0.119;PS=0.16;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-64.46,0,-50.56:5:99:37:20 1/0:-75.64,0,-92.64:8:99:54:25 9 138128055 . A G 2033 PASS Source=Platypus;CSQ=G|ENSG00000227958|ENST00000452377|Transcript|intron_variant&non_coding_transcript_variant|||||RP11-399H11.3|lincRNA|YES||||||;GR=-0.47;PH=-0.931;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/1:-239.8,-20.36,0:1:99:72:72 0/0:0,-16.26,-201.6:0:99:53:0 9 138290099 . T C 170 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-0.637;PH=-0.27;PS=0.002;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-13.49,0,-12.79:8:99:10:5 0/0:0,-2.34,-43.13:29:23:14:0 9 140223926 . G A 645 Q20 Source=Platypus;CSQ=A|ENSG00000187609|ENST00000340951|Transcript|intron_variant|||||EXD3|protein_coding|YES||||||,A|ENSG00000187609|ENST00000491734|Transcript|intron_variant&NMD_transcript_variant|||||EXD3|nonsense_mediated_decay|||||||,A|ENSG00000187609|ENST00000342129|Transcript|intron_variant|||||EXD3|protein_coding|||||||,A|ENSG00000187609|ENST00000487745|Transcript|intron_variant&non_coding_transcript_variant|||||EXD3|retained_intron|||||||,A||ENSR00001318027|RegulatoryFeature|regulatory_region_variant||||||regulatory_region||||||| GT:GL:GOF:GQ:NR:NV 1/0:-62.09,0,-56.09:3:99:41:20 1/1:-193.9,-15.91,0:2:99:57:57 X 7943706 . G A 1233 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;REPMASK=LTR;SD=0.910773 GT:GL:GOF:GQ:NR:NV 1/1:-231.1,-19.27,0:30:99:67:66 0/0:0,-16.86,-203.2:0:99:58:0 X 8540610 . AT - 1454 PASS Source=Platypus;CSQ=-|ENSG00000011201|ENST00000262648|Transcript|intron_variant&feature_truncation|||||KAL1|protein_coding|YES||||||,-|ENSG00000011201|ENST00000488294|Transcript|upstream_gene_variant||||1919|KAL1|processed_transcript|||||||;GR=0.199;PH=0.24;PS=0.493;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-1.36,0,-14.86:3:14:33:5 0/0:0,-3.22,-25.5:3:32:48:7 X 16893824 . T C 577 PASS Source=Platypus;CSQ=C|ENSG00000222736|ENST00000410804|Transcript|upstream_gene_variant||||434|RNU4-6P|snRNA|YES||||||;GR=0.392;PH=0.343;PS=0.01;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-76.95,0,-64.05:12:99:46:25 0/0:0,-17.46,-210.8:3:99:59:0 X 17432505 . TGG - 294 PASS Source=Platypus;CSQ=-|ENSG00000188158|ENST00000380060|Transcript|intron_variant&feature_truncation|||||NHS|protein_coding|YES||||||,-||ENSR00000476046|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=-1.42;PH=-0.465;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.05,-300:2:99:52:0 1/0:-11.84,0,-142.34:24:99:49:24 X 18911658 . GC - 438 PASS Source=Platypus;CSQ=-|ENSG00000044446|ENST00000473739|Transcript|downstream_gene_variant||||541|PHKA2|processed_transcript|||||||,-|ENSG00000044446|ENST00000481718|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|2546-2547||||PHKA2|processed_transcript|||||||,-|ENSG00000044446|ENST00000473597|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|421-422||||PHKA2|processed_transcript|||||||,-|ENSG00000237836|ENST00000439295|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PHKA2-AS1|antisense|||||||,-|ENSG00000044446|ENST00000469485|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|1377-1378||||PHKA2|processed_transcript|||||||,-|ENSG00000044446|ENST00000469645|Transcript|downstream_gene_variant||||1605|PHKA2|processed_transcript|||||||,-|ENSG00000044446|ENST00000379942|Transcript|frameshift_variant&missense_variant&feature_truncation|4318-4319|1218|A/X||PHKA2|protein_coding|YES||||||,-|ENSG00000237836|ENST00000452900|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||PHKA2-AS1|antisense|YES||||||;GR=5.91;PH=2.504;PS=0.967 GT:GL:GOF:GQ:NR:NV 1/1:-7.3,-0.3,0:60:5:2:2 ./.:-8.9,-0.58,0:483:7:1:1 X 19572949 . A G 721 PASS Source=Platypus;CSQ=G|ENSG00000147010|ENST00000379698|Transcript|intron_variant|||||SH3KBP1|protein_coding|||||||,G|ENSG00000147010|ENST00000397821|Transcript|intron_variant|||||SH3KBP1|protein_coding|YES||||||,G|ENSG00000147010|ENST00000379726|Transcript|intron_variant|||||SH3KBP1|protein_coding|||||||,G|ENSG00000147010|ENST00000541422|Transcript|intron_variant|||||SH3KBP1|protein_coding|||||||,G|ENSG00000147010|ENST00000379716|Transcript|intron_variant|||||SH3KBP1|protein_coding|||||||,G||ENSR00000476207|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.563;PH=0.161;PS=0.029 GT:GL:GOF:GQ:NR:NV 0/1:-75.67,0,-81.57:14:99:56:26 1/1:-190.3,-15.91,0:27:99:54:54 X 21014439 . GGC - 734 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.185;PH=0.275;PS=0.122;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-16.16,-198:32:99:56:0 1/0:-62.26,0,-46.86:27:99:39:22 X 26854933 . CT - 2256 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.149;PH=0.177;PS=0.101;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-49.9,0,-74.3:6:99:54:25 0/1:-45.59,0,-66.09:2:99:47:18 X 28185560 . AA - 717 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.23;PH=0.525;PS=0.004;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-193.4,-15.91,0:11:99:54:54 0/0:0,-15.05,-186.1:1:99:51:0 X 30516628 . A G 1019 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-2.02;PH=-0.504;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.05,-175.7:3:99:54:0 1/0:-63.14,0,-98.64:2:99:57:22 X 36320562 . A G 2135 PASS Source=Platypus;CSQ=G|ENSG00000205081|ENST00000378657|Transcript|intron_variant|||||CXorf30|protein_coding|YES||||||,G|ENSG00000205081|ENST00000378653|Transcript|intron_variant|||||CXorf30|protein_coding|||||||;GR=1.18;PH=0.095;PS=0.004 GT:GL:GOF:GQ:NR:NV 1/0:-101.33,0,-94.13:12:99:65:33 1/0:-75.64,0,-95.34:14:99:59:25 X 37955345 . ACAG - 1076 HapScore Source=Platypus;CSQ=-|ENSG00000147041|ENST00000357972|Transcript|intron_variant&feature_truncation|||||SYTL5|protein_coding|||||||,-|ENSG00000147041|ENST00000297875|Transcript|intron_variant&feature_truncation|||||SYTL5|protein_coding|||||||,-|ENSG00000250349|ENST00000465127|Transcript|intron_variant&feature_truncation|||||TM4SF2|protein_coding|YES||||||,-|ENSG00000147041|ENST00000456733|Transcript|intron_variant&feature_truncation|||||SYTL5|protein_coding|YES||||||,-||ENSR00000477324|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=1.72;PH=-0.038;PS=0 GT:GL:GOF:GQ:NR:NV 1/0:-65.75,0,-69.05:1:99:48:24 1/1:-152.6,-12.34,0:1:99:42:42 X 38583853 . C T 1528 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.108;PS=0.231;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-75.52,0,-89.55:12:99:51:22 0/0:0,-11.74,-191.9:0:99:40:0 X 38769516 . C T 1241 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.427;PS=0.123;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-56.66,0,-108.86:5:99:47:14 0/0:0,-13.25,-247:1:99:59:0 X 39581998 . GCTT - 49 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.199;PH=-0.059;PS=0 GT:GL:GOF:GQ:NR:NV 2/4:-1,-1,-1:1:99:33,33,33,33:13,13,13,13 1/3:-1,-1,-1:4:99:37,37,37,37:18,18,18,18 X 50580683 . AGCC - 2964 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=2.07;PH=0.468;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/0:0,-15.95,-186.5:1:99:53:0 0/1:-70.18,0,-52.58:6:99:42:22 X 50615432 . C T 2355 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.564;PH=0.01;PS=0.01 GT:GL:GOF:GQ:NR:NV 0/1:-28.8,0,-132.9:84:99:22:3 0/1:-44.99,0,-156.1:90:99:19:2 X 54050069 . G A 978 PASS Source=Platypus;CSQ=A|ENSG00000172943|ENST00000433120|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000453905|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000437224|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000338154|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000338946|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000396282|Transcript|upstream_gene_variant||||1374|PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000415025|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000357988|Transcript|intron_variant|||||PHF8|protein_coding|YES||||||,A|ENSG00000172943|ENST00000322659|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000425862|Transcript|intron_variant|||||PHF8|protein_coding|||||||,A|ENSG00000172943|ENST00000445025|Transcript|intron_variant|||||PHF8|protein_coding|||||||;GR=0.235;PH=0.288;PS=0.013;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/0:-92.24,0,-69.94:8:99:54:29 0/0:0,-15.65,-191.7:2:99:54:0 X 54396356 . G A 2813 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;PH=0.099;PS=0.065;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/0:-98.03,0,-89.23:1:99:66:35 1/0:-57.85,0,-104.95:2:99:54:20 X 57911422 . TT - 750 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/2:-1,-1,-1:0:99:11,10:6,4 1/1:-1,-1,-1:0:52:19,17:16,0 X 62906891 . A G 1416 PASS Source=Platypus;CSQ=G|ENSG00000131089|ENST00000374878|Transcript|intron_variant|||||ARHGEF9|protein_coding|||||||,G|ENSG00000131089|ENST00000374872|Transcript|intron_variant|||||ARHGEF9|protein_coding|||||||,G|ENSG00000131089|ENST00000374870|Transcript|intron_variant|||||ARHGEF9|protein_coding|||||||,G|ENSG00000131089|ENST00000437457|Transcript|intron_variant|||||ARHGEF9|protein_coding|||||||,G|ENSG00000131089|ENST00000495564|Transcript|intron_variant&non_coding_transcript_variant|||||ARHGEF9|processed_transcript|||||||,G|ENSG00000131089|ENST00000253401|Transcript|intron_variant|||||ARHGEF9|protein_coding|YES||||||;GR=0.149;PH=0.152;PS=0.118;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-13.55,-170.8:22:99:47:0 1/1:-202.6,-16.26,0:21:99:56:56 X 63034017 . A G 976 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.28;PH=0.277;PS=0.003 GT:GL:GOF:GQ:NR:NV 0/0:0,-12.94,-156:9:99:44:0 1/0:-61.25,0,-76.85:4:99:48:23 X 95149751 . G A 734 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.882;PH=0.119;PS=0 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.83,-159.6:6:99:44:0 0/1:-54.36,0,-45.36:4:99:37:21 X 99246139 . C T 2089 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=1.55;PH=-0.098;PS=0.009 GT:GL:GOF:GQ:NR:NV 1/1:-199.2,-16.51,0:5:99:57:57 1/1:-240,-20.12,0:3:99:71:70 X 111728438 rs184181423 C T 1358 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.147;PS=0.182;REPMASK=LINE;1000G=0.000264901 GT:GL:GOF:GQ:NR:NV 0/0:0,-86.7,-234.84:3:99:71:0 0/1:-76.15,0,-66.85:17:99:49:25 X 116313186 . G A 2170 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=0.858;PH=0.243;PS=0.001;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-240.7,-20.77,0:3:99:73:71 1/1:-247.4,-20.92,0:3:99:74:73 X 120188318 . TGTG - 819 PASS Source=Platypus;CSQ=-|ENSG00000182890|ENST00000328078|Transcript|downstream_gene_variant||||4524|GLUD2|protein_coding|YES||||||;GR=0.557;PH=0.073;PS=0.001 GT:GL:GOF:GQ:NR:NV 1/0:-81.56,0,-45.56:1:99:44:28 1/0:-58.15,0,-85.25:8:99:48:20 X 120331579 . T C 182 PASS Source=Platypus;CSQ=C||ENSR00000261375|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||,C||||intergenic_variant|||||||||||||;GR=0.225;PH=0.238;PS=0.064;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/0:0,-19.57,-235.4:11:99:66:0 1/0:-104.64,0,-88.74:8:99:66:36 X 124685524 . A G 2029 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=1.75;PH=0.947;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-77.04,0,-83.44:2:99:60:32 0/0:0,-13.85,-165.4:1:99:48:0 X 126212669 . T C 805 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.571;PH=0.426;PS=0.008;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/1:-79.96,0,-81.46:6:99:58:29 0/1:-48.18,0,-72.78:4:99:43:18 X 127531888 . G A 1788 PASS Source=Platypus;CSQ=A|ENSG00000225689|ENST00000449485|Transcript|intron_variant&non_coding_transcript_variant|||||RP1-30E17.2|lincRNA|YES||||||;GR=1.41;PH=1.014;PS=0.002 GT:GL:GOF:GQ:NR:NV 0/1:-62.65,0,-85.75:10:99:51:23 0/0:0,-14.15,-171.5:14:99:48:0 X 133931081 . GC - 1818 PASS Source=Platypus;CSQ=-|ENSG00000156504|ENST00000467413|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FAM122B|processed_transcript|||||||,-|ENSG00000156504|ENST00000493333|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||FAM122B|processed_transcript|||||||,-|ENSG00000156504|ENST00000486347|Transcript|upstream_gene_variant||||777|FAM122B|protein_coding|||||||,-|ENSG00000156504|ENST00000370790|Transcript|5_prime_UTR_variant&feature_truncation|83-84||||FAM122B|protein_coding|||||||,-|ENSG00000156504|ENST00000343004|Transcript|upstream_gene_variant||||696|FAM122B|protein_coding|YES||||||,-|ENSG00000156500|ENST00000414371|Transcript|intron_variant&feature_truncation|||||FAM122C|protein_coding|||||||,-|ENSG00000156504|ENST00000298090|Transcript|intron_variant&feature_truncation|||||FAM122B|protein_coding|||||||,-||ENSR00000073467|RegulatoryFeature|regulatory_region_variant||||||regulatory_region|||||||;GR=0.736;PH=0.256;PS=0.002 GT:GL:GOF:GQ:NR:NV 1/1:-154.2,-13.18,0:3:99:46:46 0/1:-76.57,0,-63.97:0:99:49:26 X 135118928 . TGTG - 339 PASS Source=Platypus;CSQ=-|ENSG00000198689|ENST00000370695|Transcript|intron_variant&feature_truncation|||||SLC9A6|protein_coding|YES||||||,-|ENSG00000198689|ENST00000370698|Transcript|intron_variant&feature_truncation|||||SLC9A6|protein_coding|||||||,-|ENSG00000198689|ENST00000370701|Transcript|intron_variant&feature_truncation|||||SLC9A6|protein_coding|||||||;GR=-1.66;PH=-0.599;PS=0.043;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-3.38,0,-117.08:43:34:46:2 1/0:-3.11,0,-77.51:40:31:37:4 X 137081862 . C T 1087 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=3.3;PH=0.797;PS=0.035 GT:GL:GOF:GQ:NR:NV 1/0:-53.27,0,-91.37:29:99:49:19 0/0:0,-11.14,-141.9:30:99:37:0 X 137163502 . GA - 842 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=1.5;PH=1.015;PS=0.003;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-14.12,-166.8:2:99:48:0 1/0:-118.3,0,-55.3:2:99:62:39 X 137651409 . A G 510 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=3.84;PH=1.746;PS=0.073 GT:GL:GOF:GQ:NR:NV 0/0:0,-13.21,-158.2:15:99:56:0 0/1:-28.87,0,-48.47:4:99:34:14 X 143596866 . T C 2139 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=0.812;PH=0.547;PS=0.07;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 0/0:0,-8.43,-101.3:0:84:28:0 1/1:-204.2,-16.84,0:4:99:58:58 X 144428599 . A G 1353 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;GR=-1.37;PH=-0.478;PS=0.001;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/1:-234.1,-18.64,0:2:99:64:64 1/1:-149.5,-12.04,0:0:99:41:41 X 147232111 . TT - 2849 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=5.15;PH=1.814;PS=0.343 GT:GL:GOF:GQ:NR:NV 1/1:-183.9,-15.32,0:1:99:53:52 1/1:-197.3,-16.26,0:1:99:58:57 X 153323816 . A G 1290 PASS Source=Platypus;CSQ=G|ENSG00000169057|ENST00000453960|Transcript|intron_variant|||||MECP2|protein_coding|YES||||||,G|ENSG00000169057|ENST00000496908|Transcript|intron_variant&non_coding_transcript_variant|||||MECP2|processed_transcript|||||||,G|ENSG00000169057|ENST00000369957|Transcript|intron_variant&NMD_transcript_variant|||||MECP2|nonsense_mediated_decay|||||||,G|ENSG00000169057|ENST00000486506|Transcript|upstream_gene_variant||||595|MECP2|processed_transcript|||||||,G|ENSG00000169057|ENST00000407218|Transcript|intron_variant|||||MECP2|protein_coding|||||||,G|ENSG00000169057|ENST00000415944|Transcript|intron_variant|||||MECP2|protein_coding|||||||,G|ENSG00000169057|ENST00000303391|Transcript|intron_variant|||||MECP2|protein_coding|||||||;GR=1.07;PH=0.199;PS=0.034 GT:GL:GOF:GQ:NR:NV 1/0:-77.76,0,-44.16:6:99:48:29 1/0:-48.12,0,-44.32:4:99:36:18 X 153812138 . TACA - 1512 PASS Source=Platypus;CSQ=-|ENSG00000183678|ENST00000443287|Transcript|upstream_gene_variant||||1266|CTAG1A|protein_coding|||||||,-|ENSG00000231342|ENST00000429373|Transcript|downstream_gene_variant||||1877|ATF4P2|processed_pseudogene|YES||||||,-|ENSG00000183678|ENST00000333128|Transcript|upstream_gene_variant||||1277|CTAG1A|protein_coding|YES||||||;GR=0.118;PH=0.153;PS=0.433;REPMASK=LINE;SD=0.998598 GT:GL:GOF:GQ:NR:NV 0/1:-36.94,0,-20.94:25:99:40:10 0/1:-32.41,0,-33.81:26:99:45:8 Y 4112464 . G A 72 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;GR=-3.11;PH=-1.552;PS=0;SD=0.987254 GT:GL:GOF:GQ:NR:NV 1/1:-143.7,-12.04,0:13:99:43:42 1/0:-53.3,0,-58.9:10:99:39:20 Y 5250641 . T C 2681 PASS Source=Platypus;CSQ=C|ENSG00000099715|ENST00000215473|Transcript|intron_variant|||||PCDH11Y|protein_coding|||||||,C|ENSG00000099715|ENST00000400457|Transcript|intron_variant|||||PCDH11Y|protein_coding|||||||;GR=-3.49;PH=-0.716;PS=0.005;SD=0.987938 GT:GL:GOF:GQ:NR:NV 1/1:-168.3,-13.83,0:5:99:49:49 1/1:-187.6,-16.17,0:5:99:54:53 Y 5772702 . G A 1738 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;PH=0.119;PS=0.279;REPMASK=SINE;SD=0.987771 GT:GL:GOF:GQ:NR:NV 1/1:-179.1,-15.35,0:6:99:52:52 1/1:-185.7,-15.35,0:2:99:54:54 Y 6225559 . TT - 1885 PASS Source=Platypus;CSQ=-|ENSG00000229643|ENST00000439525|Transcript|intron_variant&non_coding_transcript_variant&feature_truncation|||||LINC00280|lincRNA|YES||||||;PH=0.056;PS=0.021;SD=0.991267 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.83,-201.3:2:99:57:0 1/0:-76.31,0,-79.91:2:99:53:25 Y 6618513 . G A 863 PASS Source=Platypus;CSQ=A||||intergenic_variant|||||||||||||;REPMASK=LINE GT:GL:GOF:GQ:NR:NV 1/0:-79.76,0,-118.76:3:99:69:30 1/0:-60.55,0,-86.55:2:99:49:21 Y 6671400 . A G 2757 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;PH=0.056;PS=0.213;REPMASK=Simple_repeat GT:GL:GOF:GQ:NR:NV 0/1:-83.34,0,-80.14:3:99:57:28 0/1:-54.46,0,-72.66:2:99:42:19 Y 8853055 . A G 1170 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 1/1:-22,-4.82,0:6:48:37:19 1/0:-5.9,0,-4.8:5:48:22:11 Y 13737912 . GA - 2973 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;REPMASK=Satellite GT:GL:GOF:GQ:NR:NV 1/1:-120.3,-10.71,0:2:99:52:47 0/1:-56.32,0,-54.12:3:99:48:23 Y 14108898 . T C 1149 PASS Source=Platypus;CSQ=C|ENSG00000235649|ENST00000420610|Transcript|downstream_gene_variant||||806|MXRA5P1|unprocessed_pseudogene|YES||||||;GR=1.46;PH=0.662;PS=0.065;SD=0.913848 GT:GL:GOF:GQ:NR:NV 1/1:-258.9,-21.07,0:1:99:72:72 0/1:-71.15,0,-157.85:0:99:75:26 Y 14234061 . C T 645 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;GR=0.379;PH=0.437;PS=0.027 GT:GL:GOF:GQ:NR:NV 0/1:-140.66,0,-80.56:8:99:35:22 0/1:-185.55,0,-138.55:8:99:49:26 Y 16131677 . A G 1967 PASS Source=Platypus;CSQ=G||||intergenic_variant|||||||||||||;PH=-2.491;PS=0.007 GT:GL:GOF:GQ:NR:NV 0/0:0,-8.13,-104.3:2:81:28:0 0/1:-76.85,0,-69.95:1:99:48:25 Y 16374624 . CA - 2346 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;GR=0.255;PH=0.071;PS=0.001 GT:GL:GOF:GQ:NR:NV 0/0:0,-17.76,-216.6:0:99:61:0 1/0:-84.54,0,-92.54:1:99:58:28 Y 16376382 . T C 489 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;GR=-1.1;PH=-0.337;PS=0.022 GT:GL:GOF:GQ:NR:NV 1/0:-96.98,0,-95.48:16:99:68:36 1/0:-52.8,0,-54.4:10:99:35:18 Y 17085795 . C T 2738 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=0.064;PS=0.101;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-59.19,0,-69.29:9:99:52:25 0/0:0,-45.03,-135.6:15:99:42:0 Y 19973795 . GT - 2533 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.064;PS=0.068;REPMASK=LTR;SD=0.999885 GT:GL:GOF:GQ:NR:NV 0/1:-61.47,0,-126.07:13:99:67:24 0/0:0,-15.14,-187.1:0:99:53:0 Y 21111017 . T C 845 PASS Source=Platypus;CSQ=C|ENSG00000176728|ENST00000454875|Transcript|intron_variant&non_coding_transcript_variant|||||TTTY14|lincRNA|||||||,C|ENSG00000176728|ENST00000452584|Transcript|intron_variant&non_coding_transcript_variant|||||TTTY14|lincRNA|||||||,C|ENSG00000176728|ENST00000331787|Transcript|intron_variant&non_coding_transcript_variant|||||TTTY14|lincRNA|YES||||||;PH=0.056;PS=0.358;REPMASK=LTR GT:GL:GOF:GQ:NR:NV 0/1:-159.37,0,-214.27:5:99:132:58 0/1:-118.63,0,-217.33:2:99:113:41 Y 22520700 . AAT - 1388 PASS Source=Platypus;CSQ=-||||intergenic_variant|||||||||||||;PH=0.306;PS=0.016;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 1/1:-198.9,-15.95,0:1:99:56:55 1/1:-137.6,-10.51,0:1:99:37:36 Y 22750269 . A G 1064 PASS Source=Platypus;CSQ=G|ENSG00000198692|ENST00000382772|Transcript|intron_variant|||||EIF1AY|protein_coding|||||||,G|ENSG00000198692|ENST00000361365|Transcript|intron_variant|||||EIF1AY|protein_coding|YES||||||,G|ENSG00000198692|ENST00000485584|Transcript|intron_variant&non_coding_transcript_variant|||||EIF1AY|processed_transcript|||||||,G|ENSG00000198692|ENST00000465253|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|709||||EIF1AY|processed_transcript|||||||,G|ENSG00000198692|ENST00000464196|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant|1666||||EIF1AY|processed_transcript|||||||;PH=-1.308;PS=0.05 GT:GL:GOF:GQ:NR:NV 1/1:-151.8,-12.58,0:11:99:44:43 1/1:-105,-8.98,0:1:90:31:31 Y 22774298 . C T 2178 PASS Source=Platypus;CSQ=T||||intergenic_variant|||||||||||||;PH=-0.506;PS=0.014 GT:GL:GOF:GQ:NR:NV 1/0:-69.24,0,-107.44:2:99:62:25 0/0:0,-13.55,-164.4:2:99:46:0 Y 24363863 . CCAG - 2056 PASS Source=Platypus;CSQ=-|ENSG00000229234|ENST00000423480|Transcript|downstream_gene_variant||||1136|RBMY1KP|unprocessed_pseudogene|YES||||||;REPMASK=SINE GT:GL:GOF:GQ:NR:NV 0/1:-85.14,0,-89.84:2:99:60:29 0/1:-48.15,0,-103.35:1:99:51:19 Y 24636059 . C T 907 PASS Source=Platypus;CSQ=T|ENSG00000169789|ENST00000338793|Transcript|upstream_gene_variant||||485|PRY|protein_coding|||||||,T|ENSG00000235059|ENST00000439653|Transcript|downstream_gene_variant||||4320|AC008175.1|lincRNA|||||||,T|ENSG00000169789|ENST00000477123|Transcript|upstream_gene_variant||||485|PRY|nonsense_mediated_decay|||||||,T|ENSG00000169789|ENST00000303728|Transcript|upstream_gene_variant||||485|PRY|protein_coding|YES||||||;SD=0.999493 GT:GL:GOF:GQ:NR:NV 0/1:-43.3,0,-61.3:12:99:36:16 0/1:-58.76,0,-54.56:7:99:39:20 Y 25169167 . G A 2177 PASS Source=Platypus;CSQ=A|ENSG00000232764|ENST00000436338|Transcript|upstream_gene_variant||||2574|TRIM60P8Y|processed_pseudogene|YES||||||;PH=0.159;PS=0.005;REPMASK=LINE;SD=0.999464 GT:GL:GOF:GQ:NR:NV 1/0:-16.29,0,-4.6:5:46:45:0 1/0:-6.22,0,-24.32:6:62:49:2 Y 26423079 . GTGG - 905 PASS Source=Platypus;CSQ=-|ENSG00000248792|ENST00000509776|Transcript|upstream_gene_variant||||1746|LINC00266-2P|unprocessed_pseudogene|YES||||||,-|ENSG00000224827|ENST00000413372|Transcript|non_coding_transcript_exon_variant&non_coding_transcript_variant&feature_truncation|688-691||||LINC00265-2P|processed_pseudogene|YES||||||,-|ENSG00000233740|ENST00000420675|Transcript|downstream_gene_variant||||1402|CICP2|processed_pseudogene|YES||||||;PH=-1.258;PS=0.008;SD=0.996379 GT:GL:GOF:GQ:NR:NV 0/1:-53.33,0,-74.63:4:99:47:21 0/0:0,-10.66,-119.2:9:99:37:0 Y 27804013 . T C 1027 PASS Source=Platypus;CSQ=C||||intergenic_variant|||||||||||||;PH=0.056;PS=0.389;REPMASK=LINE;SD=0.999753 GT:GL:GOF:GQ:NR:NV 0/0:0,-19.53,-232.1:2:99:68:1 0/1:-42.6,0,-88:10:99:45:17 Y 28738301 . C T 2000 PASS Source=Platypus;CSQ=T|ENSG00000227629|ENST00000456738|Transcript|upstream_gene_variant||||553|SLC25A15P1|unprocessed_pseudogene|YES||||||,T|ENSG00000237917|ENST00000435945|Transcript|downstream_gene_variant||||2697|PARP4P1|unprocessed_pseudogene|YES||||||;GR=1.01;PH=0.883;PS=0.036;SD=0.953878 GT:GL:GOF:GQ:NR:NV 0/0:0,-16.88,-191.5:2:99:58:0 0/1:-93.16,0,-88.06:2:99:64:34