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date Tue, 03 Jul 2018 04:38:21 -0400
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##fileformat=VCFv4.1
##fileDate=20180622
##phasing=none
##reference=file:///export/galaxy/database/files/000/dataset_3.dat
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=IGT,Number=1,Type=String,Description="Genotype when called independently (only filled if called in joint prior mode)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Total read depth">
##FORMAT=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##FORMAT=<ID=BCOUNT,Number=4,Type=Integer,Description="Occurrence count for each base at this site (A,C,G,T)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=JGQ,Number=1,Type=Integer,Description="Joint genotype quality (only filled if called in join prior mode)">
##FORMAT=<ID=VAQ,Number=1,Type=Integer,Description="Variant allele quality">
##FORMAT=<ID=BQ,Number=.,Type=Integer,Description="Average base quality">
##FORMAT=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality across all reads">
##FORMAT=<ID=AMQ,Number=.,Type=Integer,Description="Average mapping quality for each allele present in the genotype">
##FORMAT=<ID=SS,Number=1,Type=Integer,Description="Variant status relative to non-adjacent Normal, 0=wildtype,1=germline,2=somatic,3=LOH,4=unknown">
##FORMAT=<ID=SSC,Number=1,Type=Integer,Description="Somatic Score">
##VEP=v86 cache=/export/tool_deps/_conda/envs/mulled-v1-c5544a4fa88c522f4b1beb0a65a70220b74d71ea68381cf90426c17c3730f692/vep_cache/homo_sapiens/86_GRCh38 db=. COSMIC=77 genebuild=2014-07 polyphen=2.2.2 assembly=GRCh38.p7 ESP=20141103 ClinVar=201607 sift=sift5.2.2 regbuild=14 gencode=GENCODE 25 dbSNP=147 HGMD-PUBLIC=20162
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOR
chr1	133129	.	G	A	.	.	CSQ=A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP27|ENSG00000233750|Transcript|ENST00000442987|processed_pseudogene|1/1||||2105|||||||1||HGNC|HGNC:48835,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000453576|lincRNA||1/1||||||||||-1||Clone_based_vega_gene|,A|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000471248|lincRNA|||||||||||3956|-1||Clone_based_vega_gene|,A|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000477740|lincRNA|||||||||||3912|-1||Clone_based_vega_gene|,A|downstream_gene_variant|MODIFIER|RP11-34P13.15|ENSG00000268903|Transcript|ENST00000494149|processed_pseudogene|||||||||||2012|-1||Clone_based_vega_gene|,A|downstream_gene_variant|MODIFIER|RP11-34P13.16|ENSG00000269981|Transcript|ENST00000595919|processed_pseudogene|||||||||||4553|-1||Clone_based_vega_gene|,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000610542|lincRNA||1/3||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:376:187,124,29,36:65,0,311,0:161:.:0:32:5:4:0:.	0/1:0/1:907:361,249,237,60:296,1,610,0:214:.:214:29,32:24:22,25:2:218
chr1	133160	.	G	A	.	.	CSQ=A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP27|ENSG00000233750|Transcript|ENST00000442987|processed_pseudogene|1/1||||2136|||||||1||HGNC|HGNC:48835,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000453576|lincRNA||1/1||||||||||-1||Clone_based_vega_gene|,A|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000471248|lincRNA|||||||||||3987|-1||Clone_based_vega_gene|,A|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000477740|lincRNA|||||||||||3943|-1||Clone_based_vega_gene|,A|downstream_gene_variant|MODIFIER|RP11-34P13.15|ENSG00000268903|Transcript|ENST00000494149|processed_pseudogene|||||||||||1981|-1||Clone_based_vega_gene|,A|downstream_gene_variant|MODIFIER|RP11-34P13.16|ENSG00000269981|Transcript|ENST00000595919|processed_pseudogene|||||||||||4522|-1||Clone_based_vega_gene|,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000610542|lincRNA||1/3||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:351:158,147,16,30:46,0,305,0:145:.:0:33:13:12:0:.	0/1:0/1:871:370,354,61,86:145,0,724,2:30:.:30:32,33:35:36,35:2:57
chr1	133483	.	G	T	.	.	CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP27|ENSG00000233750|Transcript|ENST00000442987|processed_pseudogene|1/1||||2459|||||||1||HGNC|HGNC:48835,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000453576|lincRNA|1/2||||84|||||||-1||Clone_based_vega_gene|,T|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000471248|lincRNA|||||||||||4310|-1||Clone_based_vega_gene|,T|upstream_gene_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000477740|lincRNA|||||||||||4266|-1||Clone_based_vega_gene|,T|downstream_gene_variant|MODIFIER|RP11-34P13.15|ENSG00000268903|Transcript|ENST00000494149|processed_pseudogene|||||||||||1658|-1||Clone_based_vega_gene|,T|downstream_gene_variant|MODIFIER|RP11-34P13.16|ENSG00000269981|Transcript|ENST00000595919|processed_pseudogene|||||||||||4199|-1||Clone_based_vega_gene|,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RP11-34P13.7|ENSG00000238009|Transcript|ENST00000610542|lincRNA|1/4||||241|||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:388:203,111,46,28:2,0,314,72:1:.:0:29:1:0:0:.	0/1:0/1:1101:577,245,160,119:1,0,822,278:41:.:41:29,30:11:10,14:2:71
chr1	1250144	.	T	C	.	.	CSQ=C|upstream_gene_variant|MODIFIER|FAM132A|ENSG00000184163|Transcript|ENST00000330388|protein_coding|||||||||||3422|-1||HGNC|HGNC:32308,C|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000347370|protein_coding|||||||||||3770|-1||HGNC|HGNC:19268,C|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000349431|protein_coding|||||||||||4326|-1||HGNC|HGNC:19268,C|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000400929|protein_coding|||||||||||4841|-1||HGNC|HGNC:19268,C|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000450390|nonsense_mediated_decay|||||||||||3765|-1||HGNC|HGNC:19268,C|downstream_gene_variant|MODIFIER|UBE2J2|ENSG00000160087|Transcript|ENST00000464036|nonsense_mediated_decay|||||||||||4904|-1||HGNC|HGNC:19268,C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RP5-902P8.12|ENSG00000260179|Transcript|ENST00000565563|lincRNA|1/1||||1191|||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:10:4,6,0,0:0,0,0,10:57:.:0:29:22:22:0:.	0/1:0/1:18:9,6,0,3:0,3,0,15:6:.:6:33,29:52:35,55:2:28
chr1	2280653	.	A	G	.	.	CSQ=G|intron_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000378536|protein_coding||1/6||||||||||1||HGNC|HGNC:10896,G|intron_variant&non_coding_transcript_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000478223|processed_transcript||1/2||||||||||1||HGNC|HGNC:10896,G|intron_variant&non_coding_transcript_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000508416|processed_transcript||1/1||||||||||1||HGNC|HGNC:10896	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:55:24,16,2,13:40,0,15,0:55:.:0:25:15:19:0:.	0/1:0/1:70:15,19,8,28:34,0,36,0:118:.:118:25,30:28:41,15:2:28
chr1	2280736	.	A	G	.	.	CSQ=G|intron_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000378536|protein_coding||1/6||||||||||1||HGNC|HGNC:10896,G|intron_variant&non_coding_transcript_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000478223|processed_transcript||1/2||||||||||1||HGNC|HGNC:10896,G|intron_variant&non_coding_transcript_variant|MODIFIER|SKI|ENSG00000157933|Transcript|ENST00000508416|processed_transcript||1/1||||||||||1||HGNC|HGNC:10896	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:8:2,6,0,0:8,0,0,0:51:.:0:31:18:18:0:.	0/1:0/1:8:2,3,0,3:5,0,3,0:19:.:19:27,31:25:20,34:2:24
chr1	11522650	.	G	A	.	.	CSQ=A|intron_variant|MODIFIER|DISP3|ENSG00000204624|Transcript|ENST00000294484|protein_coding||10/20||||||||||1||HGNC|HGNC:29251	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:4,2,0,0:0,0,6,0:18:.:0:30:1:1:0:.	1/1:1/1:2:0,1,0,1:1,0,1,0:3:.:3:33:35:40:2:18
chr1	57636120	.	C	A	.	.	CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|DAB1|ENSG00000173406|Transcript|ENST00000485760|processed_transcript||7/20||||||||||-1||HGNC|HGNC:2661	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:34:14,12,8,0:8,26,0,0:55:.:0:21:54:60:0:.	0/1:0/1:44:16,12,16,0:16,28,0,0:1:.:1:14,21:56:51,59:2:25
chr1	72135390	.	C	A	.	.	CSQ=A|intron_variant|MODIFIER|NEGR1|ENSG00000172260|Transcript|ENST00000357731|protein_coding||1/6||||||||||-1||HGNC|HGNC:17302	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:53:36,7,0,10:10,43,0,0:53:.:0:24:27:26:0:.	0/1:0/1:90:60,4,3,23:26,64,0,0:57:.:57:23,24:51:45,54:2:26
chr1	116600445	.	G	A	.	.	CSQ=A|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000318837|protein_coding||6/10||||||||||-1||HGNC|HGNC:5950,A|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000369483|protein_coding||7/11||||||||||-1||HGNC|HGNC:5950,A|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000369486|protein_coding||6/10||||||||||-1||HGNC|HGNC:5950	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:24:0,22,0,2:2,0,22,0:55:.:0:33:32:34:0:.	0/1:0/1:30:0,20,0,10:10,0,20,0:42:.:42:32,33:48:27,58:2:28
chr1	116600446	.	A	G	.	.	CSQ=G|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000318837|protein_coding||6/10||||||||||-1||HGNC|HGNC:5950,G|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000369483|protein_coding||7/11||||||||||-1||HGNC|HGNC:5950,G|intron_variant|MODIFIER|IGSF3|ENSG00000143061|Transcript|ENST00000369486|protein_coding||6/10||||||||||-1||HGNC|HGNC:5950	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:22:0,22,0,0:22,0,0,0:93:.:0:30:34:34:0:.	0/1:0/1:29:0,20,0,9:20,0,9,0:28:.:28:30,32:48:58,25:2:55
chr1	125167865	.	T	C	.	.	CSQ=C|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:4:3,1,0,0:0,0,0,4:14:.:0:29:0:0:0:.	1/1:1/1:1:0,0,0,1:0,1,0,0:22:.:22:34:22:22:2:16
chr1	143192820	.	G	A	.	.	CSQ=A|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:4,2,0,0:0,0,6,0:18:.:0:30:0:0:0:.	1/1:1/1:2:0,1,1,0:1,0,1,0:26:.:26:32:20:40:2:19
chr1	143192836	.	C	T	.	.	CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:4,2,0,0:0,6,0,0:18:.:0:30:0:0:0:.	1/1:1/1:2:0,1,1,0:0,1,0,1:25:.:25:31:20:40:2:18
chr1	147517696	.	C	T	.	.	CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|LINC00624|ENSG00000278811|Transcript|ENST00000619867|antisense|1/6||||180|||||||-1||HGNC|HGNC:44254,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|LINC00624|ENSG00000278811|Transcript|ENST00000621316|antisense|1/4||||180|||||||-1||HGNC|HGNC:44254	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:33:60:60:0:.	0/1:0/1:9:1,4,1,3:0,5,0,4:63:.:63:33,32:60:60,60:2:18
chr1	148359371	.	C	A	.	.	CSQ=A|downstream_gene_variant|MODIFIER|RNVU1-1|ENSG00000207340|Transcript|ENST00000384610|snRNA|||||||||||2999|-1||HGNC|HGNC:10133,A|upstream_gene_variant|MODIFIER|RP6-74O6.6|ENSG00000272824|Transcript|ENST00000609678|lincRNA|||||||||||685|-1||Clone_based_vega_gene|,A|downstream_gene_variant|MODIFIER|LINC01138|ENSG00000274020|Transcript|ENST00000622328|lincRNA|||||||||||3624|-1||HGNC|HGNC:49454	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:8:8,0,0,0:0,8,0,0:51:.:0:32:38:38:0:.	0/1:0/1:15:12,0,0,3:3,12,0,0:3:.:3:29,33:55:60,54:2:23
chr1	149390829	.	C	A	.	.	CSQ=A|5_prime_UTR_variant|MODIFIER|NBPF19|ENSG00000271383|Transcript|ENST00000621744|protein_coding|1/97||||207|||||||1||HGNC|HGNC:31999	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:33:0,12,3,18:20,12,0,1:2:.:0:27:3:8:0:.	0/1:0/1:39:1,22,1,15:16,23,0,0:20:.:20:31,25:33:12,48:2:25
chr1	151171163	.	A	G	.	.	CSQ=G|intron_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000295314|protein_coding||7/9||||||||||-1||HGNC|HGNC:11874,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000368902|protein_coding|||||||||||2025|1||HGNC|HGNC:23136,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000368905|protein_coding|||||||||||866|1||HGNC|HGNC:23136,G|downstream_gene_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000441701|protein_coding|||||||||||1166|-1|cds_end_NF|HGNC|HGNC:11874,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000459799|processed_transcript|||||||||||2030|1||HGNC|HGNC:23136,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000461862|processed_transcript|||||||||||3184|1||HGNC|HGNC:23136,G|intron_variant&NMD_transcript_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000463543|nonsense_mediated_decay||7/9||||||||||-1||HGNC|HGNC:11874,G|intron_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000466891|protein_coding||2/3||||||||||-1|cds_start_NF|HGNC|HGNC:11874,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000471039|processed_transcript|||||||||||4213|1||HGNC|HGNC:23136,G|downstream_gene_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000488488|processed_transcript|||||||||||270|-1||HGNC|HGNC:11874,G|intron_variant&non_coding_transcript_variant|MODIFIER|VPS72|ENSG00000163159|Transcript|ENST00000491094|retained_intron||10/12||||||||||-1||HGNC|HGNC:11644,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000497147|processed_transcript|||||||||||2052|1||HGNC|HGNC:23136,G|downstream_gene_variant|MODIFIER|TMOD4|ENSG00000163157|Transcript|ENST00000601585|processed_transcript|||||||||||4454|-1||HGNC|HGNC:11874,G|downstream_gene_variant|MODIFIER|SCNM1|ENSG00000163156|Transcript|ENST00000602841|protein_coding|||||||||||2030|1||HGNC|HGNC:23136	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:2:0,2,0,0:2,0,0,0:33:.:0:33:60:60:0:.	1/1:1/1:1:0,0,0,1:0,0,1,0:30:.:30:32:60:60:2:16
chr1	152303901	.	C	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||11021|10985|3662|S/T|aGt/aCt|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:563:229,216,52,66:1,445,117,0:11:.:0:32:0:0:0:.	0/1:0/1:2572:939,1036,377,220:2,1975,595,0:93:.:93:32,32:15:16,12:2:120
chr1	152303983	.	C	T	.	.	CSQ=T|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||10939|10903|3635|D/N|Gac/Aac|||-1||HGNC|HGNC:3748,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:614:273,243,43,55:0,516,0,98:73:.:0:33:3:3:0:.	0/1:0/1:2851:1013,1052,312,474:0,2065,0,786:228:.:228:33,31:28:29,27:2:247
chr1	152304107	.	C	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||10815|10779|3593|E/D|gaG/gaC|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:394:195,173,13,13:0,368,26,0:255:.:0:33:18:20:0:.	0/1:0/1:1708:624,733,200,151:0,1357,351,0:155:.:155:33,32:41:47,18:2:182
chr1	152304122	.	G	A	.	.	CSQ=A|synonymous_variant|LOW|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||10800|10764|3588|H|caC/caT|||-1||HGNC|HGNC:3748,A|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,A|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:389:186,184,5,14:19,0,370,0:255:.:0:29:23:25:0:.	0/1:0/1:1605:602,679,166,158:324,0,1281,0:114:.:114:30,29:47:16,55:2:141
chr1	152304150	.	G	C	.	.	CSQ=C|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||10772|10736|3579|T/R|aCg/aGg|||-1||HGNC|HGNC:3748,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:433:164,184,41,44:0,85,348,0:218:.:0:30:24:29:0:.	0/1:0/1:1470:533,682,135,120:0,255,1215,0:116:.:116:33,30:53:22,59:2:143
chr1	152306079	.	T	C	.	.	CSQ=C|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||8843|8807|2936|D/G|gAc/gGc|||-1||HGNC|HGNC:3748,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:578:205,203,83,87:0,170,0,408:2:.:0:31:0:0:0:.	0/1:0/1:3958:1466,1740,451,301:0,750,2,3206:203:.:203:33,31:14:19,12:2:63
chr1	152306338	.	C	T	.	.	CSQ=T|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||8584|8548|2850|G/S|Ggc/Agc|||-1||HGNC|HGNC:3748,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:411:137,165,68,41:0,302,0,109:135:.:0:30:22:27:0:.	0/1:0/1:4985:2106,2070,462,347:3,4176,2,804:228:.:228:30,32:50:54,31:2:108
chr1	152306380	.	T	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||8542|8506|2836|S/R|Agt/Cgt|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:487:206,225,32,24:0,0,56,431:203:.:0:31:10:9:0:.	0/1:0/1:5056:2043,2014,517,482:1,0,998,4057:228:.:228:29,32:36:39,35:2:228
chr1	152307694	.	C	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||7228|7192|2398|E/Q|Gag/Cag|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:537:220,192,50,75:0,412,125,0:57:.:0:33:1:1:0:.	0/1:0/1:2374:820,645,307,602:0,1465,909,0:228:.:228:32,31:22:19,27:2:145
chr1	152307789	.	C	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||7133|7097|2366|S/T|aGt/aCt|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:574:227,204,65,78:1,431,142,0:7:.:0:32:0:0:0:.	0/1:0/1:2091:717,763,159,452:2,1480,609,0:228:.:228:32,31:14:13,17:2:111
chr1	152307871	.	C	T	.	.	CSQ=T|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||7051|7015|2339|D/N|Gac/Aac|||-1||HGNC|HGNC:3748,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:445:209,207,16,13:2,416,0,27:80:.:0:33:6:6:0:.	0/1:0/1:1915:846,652,315,102:1,1498,1,415:228:.:228:33,30:28:29,23:2:250
chr1	152307896	.	G	A	.	.	CSQ=A|synonymous_variant|LOW|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||7026|6990|2330|H|caC/caT|||-1||HGNC|HGNC:3748,A|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,A|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:367:184,183,0,0:0,0,367,0:114:.:0:29:9:9:0:.	0/1:0/1:1801:593,587,615,6:620,0,1180,1:228:.:228:31,29:34:26,39:2:250
chr1	152307995	.	C	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||6927|6891|2297|E/D|gaG/gaC|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:429:173,167,41,48:0,340,89,0:135:.:0:33:15:17:0:.	0/1:0/1:3096:1236,990,353,517:1,2226,869,0:228:.:228:33,32:44:49,34:2:108
chr1	152308083	.	T	C	.	.	CSQ=C|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||6839|6803|2268|H/R|cAt/cGt|||-1||HGNC|HGNC:3748,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,C|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:422:192,182,18,30:2,46,0,374:255:.:0:31:36:41:0:.	0/1:0/1:2559:1011,1235,84,229:2,311,0,2246:64:.:64:28,31:55:26,59:2:91
chr1	152308424	.	T	G	.	.	CSQ=G|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||6498|6462|2154|Q/H|caA/caC|||-1||HGNC|HGNC:3748,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:422:170,175,45,32:0,0,77,345:64:.:0:32:37:39:0:.	0/1:0/1:3124:1059,1130,507,428:0,2,933,2189:228:.:228:29,31:55:48,58:2:37
chr1	152308814	.	A	G	.	.	CSQ=G|synonymous_variant|LOW|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||6108|6072|2024|H|caT/caC|||-1||HGNC|HGNC:3748,G|upstream_gene_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000392688|antisense|||||||||||4645|1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,G|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:424:122,174,86,42:296,1,127,0:88:.:0:31:21:27:0:.	0/1:0/1:3521:1103,1235,588,595:2338,1,1182,0:228:.:228:30,29:52:58,40:2:61
chr1	152310807	.	C	T	.	.	CSQ=T|missense_variant|MODERATE|FLG|ENSG00000143631|Transcript|ENST00000368799|protein_coding|3/3||||4115|4079|1360|R/H|cGc/cAc|||-1||HGNC|HGNC:3748,T|upstream_gene_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000392688|antisense|||||||||||2652|1||HGNC|HGNC:27913,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000420707|antisense||4/8||||||||||1||HGNC|HGNC:27913,T|intron_variant&non_coding_transcript_variant|MODIFIER|FLG-AS1|ENSG00000237975|Transcript|ENST00000593011|antisense||2/3||||||||||1||HGNC|HGNC:27913	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:394:172,150,22,50:2,322,0,70:51:.:0:30:40:40:0:.	0/1:0/1:2461:670,644,573,574:4,1314,3,1140:228:.:228:30,30:53:60,46:2:24
chr1	158607804	.	C	A	.	.	CSQ=A|downstream_gene_variant|MODIFIER|OR10Z1|ENSG00000198967|Transcript|ENST00000361284|protein_coding|||||||||||424|1||HGNC|HGNC:14996,A|downstream_gene_variant|MODIFIER|SPTA1|ENSG00000163554|Transcript|ENST00000368147|protein_coding|||||||||||2902|-1||HGNC|HGNC:11272,A|downstream_gene_variant|MODIFIER|SPTA1|ENSG00000163554|Transcript|ENST00000481212|retained_intron|||||||||||4945|-1||HGNC|HGNC:11272,A|downstream_gene_variant|MODIFIER|SPTA1|ENSG00000163554|Transcript|ENST00000485680|processed_transcript|||||||||||3404|-1||HGNC|HGNC:11272,A|downstream_gene_variant|MODIFIER|SPTA1|ENSG00000163554|Transcript|ENST00000498708|retained_intron|||||||||||4979|-1||HGNC|HGNC:11272	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:8:0,8,0,0:0,8,0,0:51:.:0:33:60:60:0:.	0/1:0/1:10:1,7,1,1:2,8,0,0:6:.:6:31,33:60:60,60:2:23
chr1	161363118	.	C	T	.	.	CSQ=T|3_prime_UTR_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000342751|protein_coding|5/5||||1056|||||||1||HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|CFAP126|ENSG00000188931|Transcript|ENST00000367974|protein_coding|||||||||||1613|-1||HGNC|HGNC:32325,T|3_prime_UTR_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000367975|protein_coding|6/6||||1344|||||||1||HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000392169|protein_coding|||||||||||685|1||HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000432287|protein_coding|||||||||||657|1||HGNC|HGNC:10682,T|upstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000437833|processed_transcript|||||||||||4904|1||HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000470743|nonsense_mediated_decay|||||||||||461|1|cds_start_NF|HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000504963|nonsense_mediated_decay|||||||||||666|1||HGNC|HGNC:10682,T|downstream_gene_variant|MODIFIER|SDHC|ENSG00000143252|Transcript|ENST00000513009|protein_coding|||||||||||578|1||HGNC|HGNC:10682	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:171:24,101,8,38:0,125,0,46:77:.:0:33:10:9:0:.	0/1:0/1:326:37,152,29,108:0,189,0,137:228:.:228:33,31:35:33,37:2:50
chr1	161444478	.	T	A	.	.	CSQ=A|upstream_gene_variant|MODIFIER|RP11-122G18.11|ENSG00000283317|Transcript|ENST00000636824|lincRNA|||||||||||3482|-1||Clone_based_vega_gene|,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-122G18.10|ENSG00000283360|Transcript|ENST00000637155|lincRNA||1/4||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:90:27,33,21,9:30,0,0,60:47:.:0:31:4:4:0:.	0/1:0/1:85:39,15,25,6:31,0,0,54:61:.:61:31,31:13:20,9:2:20
chr1	161444486	.	A	G	.	.	CSQ=G|upstream_gene_variant|MODIFIER|RP11-122G18.11|ENSG00000283317|Transcript|ENST00000636824|lincRNA|||||||||||3490|-1||Clone_based_vega_gene|,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-122G18.10|ENSG00000283360|Transcript|ENST00000637155|lincRNA||1/4||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:86:23,33,21,9:56,0,30,0:43:.:0:30:4:5:0:.	0/1:0/1:73:29,13,25,6:42,0,31,0:74:.:74:29,26:15:12,20:2:16
chr1	161444488	.	A	G	.	.	CSQ=G|upstream_gene_variant|MODIFIER|RP11-122G18.11|ENSG00000283317|Transcript|ENST00000636824|lincRNA|||||||||||3492|-1||Clone_based_vega_gene|,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-122G18.10|ENSG00000283360|Transcript|ENST00000637155|lincRNA||1/4||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:88:22,35,21,10:57,0,31,0:42:.:0:30:4:5:0:.	0/1:0/1:74:30,13,24,7:43,0,31,0:72:.:72:29,28:15:12,19:2:15
chr1	161444514	.	T	A	.	.	CSQ=A|upstream_gene_variant|MODIFIER|RP11-122G18.11|ENSG00000283317|Transcript|ENST00000636824|lincRNA|||||||||||3518|-1||Clone_based_vega_gene|,A|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-122G18.10|ENSG00000283360|Transcript|ENST00000637155|lincRNA||1/4||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:99:10,60,19,10:29,0,0,70:54:.:0:29:3:3:0:.	0/1:0/1:70:10,25,22,13:35,0,0,35:98:.:153:29,29:17:21,12:2:33
chr1	161444527	.	C	G	.	.	CSQ=G|upstream_gene_variant|MODIFIER|RP11-122G18.11|ENSG00000283317|Transcript|ENST00000636824|lincRNA|||||||||||3531|-1||Clone_based_vega_gene|,G|intron_variant&non_coding_transcript_variant|MODIFIER|RP11-122G18.10|ENSG00000283360|Transcript|ENST00000637155|lincRNA||1/4||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:125:13,90,12,10:0,103,22,0:6:.:0:32:2:1:0:.	0/1:0/1:74:15,38,12,9:0,53,21,0:85:.:85:32,31:16:14,23:2:109
chr1	178725267	.	G	A	.	.	CSQ=A|upstream_gene_variant|MODIFIER|RALGPS2|ENSG00000116191|Transcript|ENST00000324778|protein_coding|||||||||||129|1|cds_end_NF|HGNC|HGNC:30279,A|5_prime_UTR_variant|MODIFIER|RALGPS2|ENSG00000116191|Transcript|ENST00000367634|protein_coding|1/19||||121|||||||1||HGNC|HGNC:30279,A|5_prime_UTR_variant|MODIFIER|RALGPS2|ENSG00000116191|Transcript|ENST00000367635|protein_coding|1/20||||103|||||||1||HGNC|HGNC:30279,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RALGPS2|ENSG00000116191|Transcript|ENST00000495034|retained_intron|1/10||||103|||||||1||HGNC|HGNC:30279,A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|RP11-428K3.1|ENSG00000273062|Transcript|ENST00000608517|antisense|1/1||||1019|||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:10:10,0,0,0:0,0,10,0:57:.:0:28:56:56:0:.	0/1:0/1:10:7,0,1,2:3,0,7,0:25:.:25:28,28:60:60,60:2:30
chr1	203166324	.	C	T	.	.	CSQ=T|downstream_gene_variant|MODIFIER|MYBPH|ENSG00000133055|Transcript|ENST00000255416|protein_coding|||||||||||1487|-1||HGNC|HGNC:7552,T|3_prime_UTR_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000309502|protein_coding|6/6||||1816|||||||1||HGNC|HGNC:262,T|3_prime_UTR_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000337894|protein_coding|4/4||||1838|||||||1||HGNC|HGNC:262,T|3_prime_UTR_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000367235|protein_coding|3/3||||1794|||||||1||HGNC|HGNC:262,T|3_prime_UTR_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000367236|protein_coding|3/3||||2326|||||||1||HGNC|HGNC:262,T|downstream_gene_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000464019|processed_transcript|||||||||||583|1||HGNC|HGNC:262,T|downstream_gene_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000467253|processed_transcript|||||||||||209|1||HGNC|HGNC:262,T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000472535|processed_transcript|2/2||||1211|||||||1||HGNC|HGNC:262,T|downstream_gene_variant|MODIFIER|ADORA1|ENSG00000163485|Transcript|ENST00000618295|protein_coding|||||||||||262|1||HGNC|HGNC:262,T|downstream_gene_variant|MODIFIER|MYBPH|ENSG00000133055|Transcript|ENST00000621380|protein_coding|||||||||||1487|-1||HGNC|HGNC:7552	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:6,0,0,0:0,6,0,0:45:.:0:34:60:60:0:.	0/1:0/1:8:6,0,2,0:0,6,0,2:11:.:11:33,33:60:60,60:2:18
chr1	222468242	.	T	C	.	.	CSQ=C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP13|ENSG00000234419|Transcript|ENST00000422015|processed_pseudogene|1/1||||149|||||||1||HGNC|HGNC:37907	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:61:19,37,0,5:0,5,0,56:21:.:0:31:4:4:0:.	1/1:1/1:84:4,4,17,59:0,76,0,8:116:.:240:26:33:34:2:21
chr1	223947556	.	G	A	.	.	CSQ=A|upstream_gene_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|||||||||||49|1||HGNC|HGNC:37754,A|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||3838|-1||HGNC|HGNC:51732,A|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||3923|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:91:64,7,20,0:20,0,71,0:1:.:0:28:0:0:0:.	0/1:0/1:65:42,3,19,1:20,0,45,0:26:.:38:32,28:16:26,11:2:57
chr1	223947588	.	G	T	.	.	CSQ=T|upstream_gene_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|||||||||||17|1||HGNC|HGNC:37754,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||3806|-1||HGNC|HGNC:51732,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||3891|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:117:85,18,7,7:0,0,103,14:1:.:0:32:0:0:0:.	1/1:1/1:87:39,24,20,4:0,0,63,24:11:.:60:29:11:28:2:20
chr1	223947978	.	G	T	.	.	CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|1/3||||374|||||||1||HGNC|HGNC:37754,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||3416|-1||HGNC|HGNC:51732,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||3501|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:254:171,20,53,10:0,0,191,63:1:.:0:32:1:2:0:.	0/1:0/1:430:205,20,192,13:0,0,225,205:225:.:225:32,30:35:39,31:2:134
chr1	223948062	.	G	A	.	.	CSQ=A|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|1/3||||458|||||||1||HGNC|HGNC:37754,A|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||3332|-1||HGNC|HGNC:51732,A|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||3417|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:304:132,66,44,62:104,0,198,2:62:.:0:29:20:30:0:.	0/1:0/1:1124:380,206,360,178:537,0,586,1:228:.:228:31,29:47:36,58:2:35
chr1	223948558	.	C	T	.	.	CSQ=T|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|1/3||||954|||||||1||HGNC|HGNC:37754,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||2836|-1||HGNC|HGNC:51732,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||2921|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:40:8,27,1,4:0,35,0,5:1:.:0:28:1:1:0:.	0/1:0/1:154:10,64,21,59:0,74,0,80:176:.:220:28,31:22:23,22:2:49
chr1	223949699	.	T	C	.	.	CSQ=C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|2/3||||1941|||||||1||HGNC|HGNC:37754,C|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||1695|-1||HGNC|HGNC:51732,C|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||1780|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:189:94,95,0,0:0,0,0,189:28:.:0:30:1:1:0:.	0/1:0/1:370:104,102,99,65:0,164,0,206:206:.:206:30,31:25:18,30:2:233
chr1	223950486	.	C	T	.	.	CSQ=T|downstream_gene_variant|MODIFIER|CICP5|ENSG00000233771|Transcript|ENST00000424045|unprocessed_pseudogene|||||||||||70|1||HGNC|HGNC:37754,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000608760|retained_intron|||||||||||908|-1||HGNC|HGNC:51732,T|downstream_gene_variant|MODIFIER|GTF2IP20|ENSG00000272645|Transcript|ENST00000634905|processed_transcript|||||||||||993|-1||HGNC|HGNC:51732	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:79:14,4,49,12:0,18,0,61:58:.:0:30:10:31:0:.	0/1:0/1:115:19,6,52,38:0,25,0,90:73:.:177:30,30:31:56,25:2:31
chr1	227976709	.	T	C	.	.	CSQ=C|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP26|ENSG00000233003|Transcript|ENST00000425003|unprocessed_pseudogene|1/3||||1485|||||||-1||HGNC|HGNC:48834,C|upstream_gene_variant|MODIFIER|SEPT14P17|ENSG00000274886|Transcript|ENST00000617978|unprocessed_pseudogene|||||||||||3342|1||HGNC|HGNC:51703	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:10:8,2,0,0:0,0,0,10:22:.:0:25:1:1:0:.	1/1:1/1:91:3,1,82,5:0,86,1,4:25:.:25:32:3:2:2:20
chr1	227977309	.	A	G	.	.	CSQ=G|non_coding_transcript_exon_variant&non_coding_transcript_variant|MODIFIER|CICP26|ENSG00000233003|Transcript|ENST00000425003|unprocessed_pseudogene|1/3||||885|||||||-1||HGNC|HGNC:48834,G|upstream_gene_variant|MODIFIER|SEPT14P17|ENSG00000274886|Transcript|ENST00000617978|unprocessed_pseudogene|||||||||||2742|1||HGNC|HGNC:51703	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:170:101,30,27,12:131,0,38,1:116:.:0:31:9:11:0:.	0/1:0/1:461:185,51,194,31:236,0,225,0:228:.:228:31,28:38:48,27:2:113
chr1	234978406	.	C	G	.	.	CSQ=G|downstream_gene_variant|MODIFIER|RP11-443B7.3|ENSG00000258082|Transcript|ENST00000549744|lincRNA|||||||||||1241|-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:2:2,0,0,0:0,2,0,0:33:.:0:32:60:60:0:.	1/1:1/1:1:0,0,1,0:0,0,1,0:12:.:12:12:60:60:2:15
chr1	234978426	.	C	G	.	.	CSQ=G|downstream_gene_variant|MODIFIER|RP11-443B7.3|ENSG00000258082|Transcript|ENST00000549744|lincRNA|||||||||||1221|-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:2:2,0,0,0:0,2,0,0:33:.:0:31:60:60:0:.	1/1:1/1:1:0,0,1,0:0,0,1,0:30:.:30:35:60:60:2:16
chr1	234978429	.	T	C	.	.	CSQ=C|downstream_gene_variant|MODIFIER|RP11-443B7.3|ENSG00000258082|Transcript|ENST00000549744|lincRNA|||||||||||1218|-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:2:2,0,0,0:0,0,0,2:33:.:0:34:60:60:0:.	1/1:1/1:1:0,0,1,0:0,1,0,0:25:.:25:25:60:60:2:16
chr1	240207797	.	G	A	.	.	CSQ=A|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3215|2985|995|A|gcG/gcA|||1||HGNC|HGNC:14074,A|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||610|1|cds_end_NF|HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:161:61,72,12,16:26,2,133,0:59:.:0:28:20:18:0:.	0/1:0/1:245:67,113,13,52:64,1,180,0:34:.:34:30,28:38:47,35:2:32
chr1	240207800	.	C	A	.	.	CSQ=A|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3218|2988|996|G|ggC/ggA|||1||HGNC|HGNC:14074,A|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||613|1|cds_end_NF|HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:152:57,69,12,14:22,126,4,0:95:.:0:30:18:17:0:.	0/1:0/1:225:60,107,14,44:53,167,5,0:8:.:8:30,29:37:45,34:2:35
chr1	240207806	.	C	T	.	.	CSQ=T|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3224|2994|998|P|ccC/ccT|||1||HGNC|HGNC:14074,T|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||619|1|cds_end_NF|HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:144:57,65,10,12:1,122,0,21:114:.:0:32:15:14:0:.	0/1:0/1:216:59,105,12,40:1,164,0,51:13:.:13:31,29:34:31,45:2:40
chr1	240207812	.	G	A,T	.	.	CSQ=A|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3230|3000|1000|P|ccG/ccA|||1||HGNC|HGNC:14074,T|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3230|3000|1000|P|ccG/ccT|||1||HGNC|HGNC:14074,A|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||625|1|cds_end_NF|HGNC|HGNC:14074,T|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||625|1|cds_end_NF|HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/2:0/2:124:22,15,33,54:12,8,37,67:37:.:69:21,26:10:5,12:1:.	1/2:1/2:185:12,4,50,119:31,10,16,128:95:.:165:27,26:28:38,27:2:69
chr1	240208175	.	T	G	.	.	CSQ=G|synonymous_variant|LOW|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding|5/18||||3593|3363|1121|P|ccT/ccG|||1||HGNC|HGNC:14074,G|downstream_gene_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000447095|protein_coding|||||||||||988|1|cds_end_NF|HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:125:51,50,10,14:0,7,17,101:155:.:0:28:31:36:0:.	0/1:0/1:146:64,47,12,23:0,5,30,111:2:.:2:29,27:47:24,53:2:29
chr1	240472659	.	G	T	.	.	CSQ=T|intron_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000319653|protein_coding||17/17||||||||||1||HGNC|HGNC:14074,T|intron_variant&non_coding_transcript_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000496950|processed_transcript||2/2||||||||||1||HGNC|HGNC:14074,T|intron_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000543681|protein_coding||2/2||||||||||1||HGNC|HGNC:14074,T|intron_variant|MODIFIER|FMN2|ENSG00000155816|Transcript|ENST00000545751|protein_coding||10/10||||||||||1||HGNC|HGNC:14074	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:0,6,0,0:0,0,6,0:45:.:0:25:60:60:0:.	0/1:0/1:7:0,5,0,2:0,0,5,2:8:.:8:28,30:60:60,60:2:18
chr1	242810191	.	T	G	.	.	CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:71:26,30,3,12:0,0,15,56:88:.:0:30:18:22:0:.	0/1:0/1:171:59,40,54,18:0,0,72,99:219:.:219:31,30:39:35,42:2:61
chr1	242810198	.	T	G	.	.	CSQ=G|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:79:24,34,3,18:0,0,21,58:76:.:0:30:16:21:0:.	0/1:0/1:177:57,38,54,28:0,0,82,95:228:.:228:30,30:39:35,42:2:49
chr1	243052907	.	C	T	.	.	CSQ=T|upstream_gene_variant|MODIFIER|LINC01347|ENSG00000231512|Transcript|ENST00000437691|lincRNA|||||||||||655|-1||EntrezGene|HGNC:50566,T|downstream_gene_variant|MODIFIER|RP11-261C10.7|ENSG00000253326|Transcript|ENST00000517560|processed_pseudogene|||||||||||1954|-1||Clone_based_vega_gene|,T|downstream_gene_variant|MODIFIER|RP11-261C10.8|ENSG00000278455|Transcript|ENST00000611420|processed_pseudogene|||||||||||1288|1||Clone_based_vega_gene|,T|downstream_gene_variant|MODIFIER|LINC01347|ENSG00000214837|Transcript|ENST00000627498|processed_transcript|||||||||||3400|-1||HGNC|HGNC:50566	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:7:0,7,0,0:0,7,0,0:15:.:0:25:0:0:0:.	0/1:0/1:17:0,11,0,6:0,11,0,6:23:.:23:28,31:25:26,24:2:21
chr1	244891249	.	C	T	.	.	CSQ=T|intergenic_variant|MODIFIER||||||||||||||||||||	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:30:60:60:0:.	0/1:0/1:7:0,5,0,2:0,5,0,2:4:.:4:22,28:54:60,40:2:18
chr2	3035112	.	T	C	.	.	CSQ=C|intron_variant&non_coding_transcript_variant|MODIFIER|LINC01250|ENSG00000234423|Transcript|ENST00000457478|lincRNA||3/6||||||||||-1||HGNC|HGNC:49844	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:263:82,120,30,31:0,59,2,202:64:.:0:29:49:57:0:.	0/1:0/1:559:136,265,60,98:0,157,1,401:167:.:167:27,30:53:35,60:2:37
chr2	3329166	.	G	C	.	.	CSQ=C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000382125|protein_coding||3/8||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000398659|protein_coding||3/9||||||||||-1||HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000406835|nonsense_mediated_decay||4/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000435721|nonsense_mediated_decay||3/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000441271|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000443925|protein_coding||3/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000444776|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000455162|nonsense_mediated_decay||2/6||||||||||-1||HGNC|HGNC:12383,C|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000463662|processed_transcript||3/5||||||||||-1||HGNC|HGNC:12383	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:66:24,30,6,6:0,12,54,0:73:.:0:31:28:32:0:.	0/1:0/1:64:19,28,10,7:0,13,47,4:19:.:19:28,31:39:23,47:2:43
chr2	3329223	.	G	C	.	.	CSQ=C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000382125|protein_coding||3/8||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000398659|protein_coding||3/9||||||||||-1||HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000406835|nonsense_mediated_decay||4/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000435721|nonsense_mediated_decay||3/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000441271|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000443925|protein_coding||3/5||||||||||-1||HGNC|HGNC:12383,C|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000444776|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,C|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000455162|nonsense_mediated_decay||2/6||||||||||-1||HGNC|HGNC:12383,C|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000463662|processed_transcript||3/5||||||||||-1||HGNC|HGNC:12383	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:34:11,16,5,2:0,7,27,0:51:.:0:32:34:43:0:.	0/1:0/1:36:9,13,6,8:0,7,22,7:0:.:76:30,31:42:29,51:2:27
chr2	3329230	.	G	A	.	.	CSQ=A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000382125|protein_coding||3/8||||||||||-1||HGNC|HGNC:12383,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000398659|protein_coding||3/9||||||||||-1||HGNC|HGNC:12383,A|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000406835|nonsense_mediated_decay||4/5||||||||||-1||HGNC|HGNC:12383,A|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000435721|nonsense_mediated_decay||3/5||||||||||-1||HGNC|HGNC:12383,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000441271|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000443925|protein_coding||3/5||||||||||-1||HGNC|HGNC:12383,A|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000444776|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,A|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000455162|nonsense_mediated_decay||2/6||||||||||-1||HGNC|HGNC:12383,A|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000463662|processed_transcript||3/5||||||||||-1||HGNC|HGNC:12383	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:30:9,12,7,2:7,0,21,2:44:.:0:32:35:46:0:.	0/1:0/1:31:8,10,5,8:12,0,18,1:116:.:116:30,31:44:31,52:2:17
chr2	3329243	.	A	G	.	.	CSQ=G|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000382125|protein_coding||3/8||||||||||-1||HGNC|HGNC:12383,G|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000398659|protein_coding||3/9||||||||||-1||HGNC|HGNC:12383,G|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000406835|nonsense_mediated_decay||4/5||||||||||-1||HGNC|HGNC:12383,G|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000435721|nonsense_mediated_decay||3/5||||||||||-1||HGNC|HGNC:12383,G|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000441271|protein_coding||1/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,G|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000443925|protein_coding||3/5||||||||||-1||HGNC|HGNC:12383,G|intron_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000444776|protein_coding||3/4||||||||||-1|cds_end_NF|HGNC|HGNC:12383,G|intron_variant&NMD_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000455162|nonsense_mediated_decay||2/6||||||||||-1||HGNC|HGNC:12383,G|intron_variant&non_coding_transcript_variant|MODIFIER|TSSC1|ENSG00000032389|Transcript|ENST00000463662|processed_transcript||3/5||||||||||-1||HGNC|HGNC:12383	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:29:13,14,0,2:27,0,2,0:68:.:0:30:34:36:0:.	0/1:0/1:31:9,11,2,9:20,0,11,0:59:.:59:30,31:39:48,22:2:41
chr2	3775131	.	G	C	.	.	CSQ=C|intron_variant|MODIFIER|DCDC2C|ENSG00000214866|Transcript|ENST00000399143|protein_coding||8/10||||||||||1||HGNC|HGNC:32696,C|intron_variant|MODIFIER|DCDC2C|ENSG00000214866|Transcript|ENST00000423741|protein_coding||8/8||||||||||1|cds_start_NF&cds_end_NF|HGNC|HGNC:32696,C|intron_variant&non_coding_transcript_variant|MODIFIER|DCDC2C|ENSG00000214866|Transcript|ENST00000537457|processed_transcript||5/7||||||||||1||HGNC|HGNC:32696	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:172:79,50,25,18:0,43,129,0:117:.:0:30:33:42:0:.	0/1:0/1:366:184,70,41,71:0,112,254,0:48:.:48:32,30:39:21,47:2:75
chr2	10080680	.	C	T	.	.	CSQ=T|upstream_gene_variant|MODIFIER|CYS1|ENSG00000205795|Transcript|ENST00000381813|protein_coding|||||||||||269|-1||HGNC|HGNC:18525,T|upstream_gene_variant|MODIFIER|AC104794.4|ENSG00000233502|Transcript|ENST00000425235|lincRNA|||||||||||3101|1||Clone_based_vega_gene|,T|intron_variant&non_coding_transcript_variant|MODIFIER|CYS1|ENSG00000205795|Transcript|ENST00000477304|processed_transcript||1/2||||||||||-1||HGNC|HGNC:18525	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:6,0,0,0:0,6,0,0:45:.:0:34:60:60:0:.	0/1:0/1:5:3,0,2,0:0,3,0,2:18:.:18:34,32:60:60,60:2:18
chr2	19985338	.	C	T	.	.	CSQ=T|intron_variant|MODIFIER|WDR35|ENSG00000118965|Transcript|ENST00000281405|protein_coding||2/26||||||||||-1||HGNC|HGNC:29250,T|intron_variant|MODIFIER|WDR35|ENSG00000118965|Transcript|ENST00000345530|protein_coding||2/27||||||||||-1||HGNC|HGNC:29250,T|intron_variant&NMD_transcript_variant|MODIFIER|WDR35|ENSG00000118965|Transcript|ENST00000414212|nonsense_mediated_decay||2/27||||||||||-1||HGNC|HGNC:29250,T|upstream_gene_variant|MODIFIER|AC079145.4|ENSG00000227210|Transcript|ENST00000416575|antisense|||||||||||4879|1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:41:18,5,0,18:2,23,0,16:45:.:0:32:17:24:0:.	0/1:0/1:32:15,5,0,12:1,20,0,11:14:.:14:32,28:23:27,15:2:18
chr2	39404606	.	C	T	.	.	CSQ=T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000263881|protein_coding||1/33||||||||||-1||HGNC|HGNC:6865,T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000341681|protein_coding||1/32||||||||||-1||HGNC|HGNC:6865,T|intron_variant&NMD_transcript_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000429397|nonsense_mediated_decay||1/6||||||||||-1||HGNC|HGNC:6865,T|intron_variant&NMD_transcript_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000437968|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:6865,T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000484274|protein_coding||1/2||||||||||-1||HGNC|HGNC:6865	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:24:40:40:0:.	0/1:0/1:10:0,6,0,4:0,6,0,4:30:.:30:28,26:50:57,39:2:18
chr2	39404609	.	C	T	.	.	CSQ=T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000263881|protein_coding||1/33||||||||||-1||HGNC|HGNC:6865,T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000341681|protein_coding||1/32||||||||||-1||HGNC|HGNC:6865,T|intron_variant&NMD_transcript_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000429397|nonsense_mediated_decay||1/6||||||||||-1||HGNC|HGNC:6865,T|intron_variant&NMD_transcript_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000437968|nonsense_mediated_decay||1/3||||||||||-1||HGNC|HGNC:6865,T|intron_variant|MODIFIER|MAP4K3|ENSG00000011566|Transcript|ENST00000484274|protein_coding||1/2||||||||||-1||HGNC|HGNC:6865	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:6:0,6,0,0:0,6,0,0:45:.:0:31:40:40:0:.	0/1:0/1:9:0,5,0,4:0,5,0,4:7:.:7:32,17:49:56,39:2:18
chr2	68306124	.	C	A	.	.	CSQ=A|intron_variant|MODIFIER|CNRIP1|ENSG00000119865|Transcript|ENST00000263655|protein_coding||2/2||||||||||-1||HGNC|HGNC:24546,A|intron_variant|MODIFIER|CNRIP1|ENSG00000119865|Transcript|ENST00000409559|protein_coding||2/2||||||||||-1||HGNC|HGNC:24546,A|intron_variant&non_coding_transcript_variant|MODIFIER|CNRIP1|ENSG00000119865|Transcript|ENST00000481714|processed_transcript||3/3||||||||||-1||HGNC|HGNC:24546	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:8:8,0,0,0:0,8,0,0:51:.:0:32:60:60:0:.	0/1:0/1:8:6,0,0,2:2,6,0,0:3:.:3:29,32:57:50,59:2:23
chr2	86942193	.	T	G	.	.	CSQ=G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000398193|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000409776|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000559485|protein_coding||1/22||||||||||1||HGNC|HGNC:32414	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:279:133,92,27,27:0,0,54,225:31:.:0:32:2:2:0:.	0/1:0/1:771:252,262,121,136:0,1,256,514:228:.:228:31,31:17:21,16:2:213
chr2	86942348	.	C	G	.	.	CSQ=G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000398193|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000409776|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000559485|protein_coding||1/22||||||||||1||HGNC|HGNC:32414	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:141:12,100,4,25:0,112,29,0:12:.:0:26:2:2:0:.	0/1:0/1:265:11,176,5,73:0,187,78,0:11:.:11:26,32:26:25,27:2:38
chr2	86942392	.	C	G	.	.	CSQ=G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000398193|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000409776|protein_coding||1/22||||||||||1||HGNC|HGNC:32414,G|intron_variant|MODIFIER|RGPD1|ENSG00000187627|Transcript|ENST00000559485|protein_coding||1/22||||||||||1||HGNC|HGNC:32414	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:21:0,16,0,5:0,16,5,0:1:.:0:23:0:0:0:.	0/1:0/1:41:0,32,0,9:0,32,9,0:12:.:12:27,29:19:15,31:2:21
chr2	89625699	.	G	A	.	.	CSQ=A|intron_variant&non_coding_transcript_variant|MODIFIER|RP4-614C10.3|ENSG00000283132|Transcript|ENST00000636037|unprocessed_pseudogene||6/8||||||||||-1||Clone_based_vega_gene|	GT:IGT:DP:DP4:BCOUNT:GQ:JGQ:VAQ:BQ:MQ:AMQ:SS:SSC	0/0:0/0:201:108,46,32,15:47,0,154,0:1:.:0:32:0:0:0:.	0/1:0/1:393:143,74,110,66:176,0,217,0:141:.:146:30,32:8:11,7:2:125