##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[bam/M10478.conc.on.pos.realigned.bam, bam/M10475.conc.on.pos.realigned.bam, bam/M10500.conc.on.pos.realigned.bam, bam/M128215.conc.on.pos.realigned.bam] read_buffer_size=null phone_home=STANDARD read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa rodBind=[] nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=10 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 multiallelic=false max_alternate_alleles=5 min_indel_count_for_genotyping=5 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=45.0 indelHaplotypeSize=80 bandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621,assembly=hg19>
##contig=<ID=chr10,length=135534747,assembly=hg19>
##contig=<ID=chr11,length=135006516,assembly=hg19>
##contig=<ID=chr11_gl000202_random,length=40103,assembly=hg19>
##contig=<ID=chr12,length=133851895,assembly=hg19>
##contig=<ID=chr13,length=115169878,assembly=hg19>
##contig=<ID=chr14,length=107349540,assembly=hg19>
##contig=<ID=chr15,length=102531392,assembly=hg19>
##contig=<ID=chr16,length=90354753,assembly=hg19>
##contig=<ID=chr17,length=81195210,assembly=hg19>
##contig=<ID=chr17_ctg5_hap1,length=1680828,assembly=hg19>
##contig=<ID=chr17_gl000203_random,length=37498,assembly=hg19>
##contig=<ID=chr17_gl000204_random,length=81310,assembly=hg19>
##contig=<ID=chr17_gl000205_random,length=174588,assembly=hg19>
##contig=<ID=chr17_gl000206_random,length=41001,assembly=hg19>
##contig=<ID=chr18,length=78077248,assembly=hg19>
##contig=<ID=chr18_gl000207_random,length=4262,assembly=hg19>
##contig=<ID=chr19,length=59128983,assembly=hg19>
##contig=<ID=chr19_gl000208_random,length=92689,assembly=hg19>
##contig=<ID=chr19_gl000209_random,length=159169,assembly=hg19>
##contig=<ID=chr1_gl000191_random,length=106433,assembly=hg19>
##contig=<ID=chr1_gl000192_random,length=547496,assembly=hg19>
##contig=<ID=chr2,length=243199373,assembly=hg19>
##contig=<ID=chr20,length=63025520,assembly=hg19>
##contig=<ID=chr21,length=48129895,assembly=hg19>
##contig=<ID=chr21_gl000210_random,length=27682,assembly=hg19>
##contig=<ID=chr22,length=51304566,assembly=hg19>
##contig=<ID=chr3,length=198022430,assembly=hg19>
##contig=<ID=chr4,length=191154276,assembly=hg19>
##contig=<ID=chr4_ctg9_hap1,length=590426,assembly=hg19>
##contig=<ID=chr4_gl000193_random,length=189789,assembly=hg19>
##contig=<ID=chr4_gl000194_random,length=191469,assembly=hg19>
##contig=<ID=chr5,length=180915260,assembly=hg19>
##contig=<ID=chr6,length=171115067,assembly=hg19>
##contig=<ID=chr6_apd_hap1,length=4622290,assembly=hg19>
##contig=<ID=chr6_cox_hap2,length=4795371,assembly=hg19>
##contig=<ID=chr6_dbb_hap3,length=4610396,assembly=hg19>
##contig=<ID=chr6_mann_hap4,length=4683263,assembly=hg19>
##contig=<ID=chr6_mcf_hap5,length=4833398,assembly=hg19>
##contig=<ID=chr6_qbl_hap6,length=4611984,assembly=hg19>
##contig=<ID=chr6_ssto_hap7,length=4928567,assembly=hg19>
##contig=<ID=chr7,length=159138663,assembly=hg19>
##contig=<ID=chr7_gl000195_random,length=182896,assembly=hg19>
##contig=<ID=chr8,length=146364022,assembly=hg19>
##contig=<ID=chr8_gl000196_random,length=38914,assembly=hg19>
##contig=<ID=chr8_gl000197_random,length=37175,assembly=hg19>
##contig=<ID=chr9,length=141213431,assembly=hg19>
##contig=<ID=chr9_gl000198_random,length=90085,assembly=hg19>
##contig=<ID=chr9_gl000199_random,length=169874,assembly=hg19>
##contig=<ID=chr9_gl000200_random,length=187035,assembly=hg19>
##contig=<ID=chr9_gl000201_random,length=36148,assembly=hg19>
##contig=<ID=chrM,length=16571,assembly=hg19>
##contig=<ID=chrUn_gl000211,length=166566,assembly=hg19>
##contig=<ID=chrUn_gl000212,length=186858,assembly=hg19>
##contig=<ID=chrUn_gl000213,length=164239,assembly=hg19>
##contig=<ID=chrUn_gl000214,length=137718,assembly=hg19>
##contig=<ID=chrUn_gl000215,length=172545,assembly=hg19>
##contig=<ID=chrUn_gl000216,length=172294,assembly=hg19>
##contig=<ID=chrUn_gl000217,length=172149,assembly=hg19>
##contig=<ID=chrUn_gl000218,length=161147,assembly=hg19>
##contig=<ID=chrUn_gl000219,length=179198,assembly=hg19>
##contig=<ID=chrUn_gl000220,length=161802,assembly=hg19>
##contig=<ID=chrUn_gl000221,length=155397,assembly=hg19>
##contig=<ID=chrUn_gl000222,length=186861,assembly=hg19>
##contig=<ID=chrUn_gl000223,length=180455,assembly=hg19>
##contig=<ID=chrUn_gl000224,length=179693,assembly=hg19>
##contig=<ID=chrUn_gl000225,length=211173,assembly=hg19>
##contig=<ID=chrUn_gl000226,length=15008,assembly=hg19>
##contig=<ID=chrUn_gl000227,length=128374,assembly=hg19>
##contig=<ID=chrUn_gl000228,length=129120,assembly=hg19>
##contig=<ID=chrUn_gl000229,length=19913,assembly=hg19>
##contig=<ID=chrUn_gl000230,length=43691,assembly=hg19>
##contig=<ID=chrUn_gl000231,length=27386,assembly=hg19>
##contig=<ID=chrUn_gl000232,length=40652,assembly=hg19>
##contig=<ID=chrUn_gl000233,length=45941,assembly=hg19>
##contig=<ID=chrUn_gl000234,length=40531,assembly=hg19>
##contig=<ID=chrUn_gl000235,length=34474,assembly=hg19>
##contig=<ID=chrUn_gl000236,length=41934,assembly=hg19>
##contig=<ID=chrUn_gl000237,length=45867,assembly=hg19>
##contig=<ID=chrUn_gl000238,length=39939,assembly=hg19>
##contig=<ID=chrUn_gl000239,length=33824,assembly=hg19>
##contig=<ID=chrUn_gl000240,length=41933,assembly=hg19>
##contig=<ID=chrUn_gl000241,length=42152,assembly=hg19>
##contig=<ID=chrUn_gl000242,length=43523,assembly=hg19>
##contig=<ID=chrUn_gl000243,length=43341,assembly=hg19>
##contig=<ID=chrUn_gl000244,length=39929,assembly=hg19>
##contig=<ID=chrUn_gl000245,length=36651,assembly=hg19>
##contig=<ID=chrUn_gl000246,length=38154,assembly=hg19>
##contig=<ID=chrUn_gl000247,length=36422,assembly=hg19>
##contig=<ID=chrUn_gl000248,length=39786,assembly=hg19>
##contig=<ID=chrUn_gl000249,length=38502,assembly=hg19>
##contig=<ID=chrX,length=155270560,assembly=hg19>
##contig=<ID=chrY,length=59373566,assembly=hg19>
##reference=file:///m/cphg-quinlan/cphg-quinlan/shared/genomes/hg19/bwa/gatk/hg19_gatk.fa
##SnpEffVersion="SnpEff 3.0g (build 2012-08-31), by Pablo Cingolani"
##SnpEffCmd="SnpEff  -i vcf -o vcf GRCh37.66 test4.vep.vcf "
##INFO=<ID=EFF,Number=.,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Gene_BioType | Coding | Transcript | Exon [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence type as predicted by VEP. Format: Consequence|Codons|Amino_acids|Gene|SYMBOL|Feature|EXON|PolyPhen|SIFT|Protein_position|BIOTYPE|ALLELE_NUM">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	M10475	M10478	M10500	M128215
chr10	1142208	.	T	C	3404.3	.	AC=8;AF=1.00;AN=8;DP=122;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=2.6747;MQ=36.00;MQ0=0;QD=27.90;EFF=DOWNSTREAM(MODIFIER||||208|WDR37|protein_coding|CODING|ENST00000436154|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000263150|),INTRON(MODIFIER||||494|WDR37|protein_coding|CODING|ENST00000358220|),STOP_LOST(HIGH|MISSENSE|Tga/Cga|*250R|249|WDR37|protein_coding|CODING|ENST00000381329|exon_10_1142110_1142566);CSQ=intron_variant|||ENSG00000047056|WDR37|ENST00000263150||||-/494|protein_coding|1,downstream_gene_variant|||ENSG00000047056|WDR37|ENST00000436154||||-/209|protein_coding|1,intron_variant|||ENSG00000047056|WDR37|ENST00000358220||||-/494|protein_coding|1,stop_lost|Tga/Cga|*/R|ENSG00000047056|WDR37|ENST00000381329|9/9|||250/249|protein_coding|1	GT:AD:DP:GQ:PL	1/1:1,37:39:87.16:940,87,0	1/1:0,29:29:78.20:899,78,0	1/1:0,24:24:66.14:729,66,0	1/1:0,30:30:75.18:836,75,0
chr10	48003992	.	C	T	1047.87	.	AC=4;AF=0.50;AN=8;BaseQRankSum=-0.053;DP=165;Dels=0.00;FS=6.377;HRun=0;HaplotypeScore=4.3830;MQ=20.94;MQ0=0;MQRankSum=-0.368;QD=9.53;ReadPosRankSum=1.346;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C540Y|610|ASAH2C|protein_coding|CODING|ENST00000420079|exon_10_48003968_48004056),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGt/tAt|C552Y|622|ASAH2C|protein_coding|CODING|ENST00000426610|exon_10_48003968_48004056);CSQ=missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000420079|16/17|benign(0)|tolerated(1)|542/612|protein_coding|1,missense_variant|tGt/tAt|C/Y|ENSG00000072444|ASAH2C|ENST00000426610|17/18|benign(0)|tolerated(1)|552/622|protein_coding|1	GT:AD:DP:GQ:PL	1/1:0,28:28:56.88:461,57,0	0/1:20,18:38:99:317,0,370	0/1:24,20:44:99:319,0,361	0/0:55,0:55:99:0,105,865
chr10	52004315	.	T	C	40.11	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=20.06;EFF=INTRON(MODIFIER||||240|ASAH2|protein_coding|CODING|ENST00000374028|),INTRON(MODIFIER||||726|ASAH2|protein_coding|CODING|ENST00000329428|),INTRON(MODIFIER||||745|ASAH2|protein_coding|CODING|ENST00000447815|),INTRON(MODIFIER||||780|ASAH2|protein_coding|CODING|ENST00000395526|),UPSTREAM(MODIFIER||||622|ASAH2|protein_coding|CODING|ENST00000443575|);CSQ=intron_variant|||ENSG00000188611|ASAH2|ENST00000329428||||-/726|protein_coding|1,upstream_gene_variant|||ENSG00000188611|ASAH2|ENST00000443575||||-/622|protein_coding|1,intron_variant|||ENSG00000188611|ASAH2|ENST00000447815||||-/745|protein_coding|1,intron_variant|||ENSG00000188611|ASAH2|ENST00000395526||||-/780|protein_coding|1	GT:AD:DP:GQ:PL	./.	./.	1/1:0,1:1:3.01:36,3,0	1/1:0,1:1:3.01:37,3,0
chr10	52497529	.	G	C	33.61	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.0000;MQ=31.58;MQ0=0;QD=16.81;EFF=UPSTREAM(MODIFIER||||160|ASAH2B|protein_coding|CODING|ENST00000185907|),UPSTREAM(MODIFIER||||160|ASAH2B|protein_coding|CODING|ENST00000374007|),UPSTREAM(MODIFIER||||165|ASAH2B|protein_coding|CODING|ENST00000374006|),UPSTREAM(MODIFIER|||||ASAH2B|processed_transcript|CODING|ENST00000483649|);CSQ=upstream_gene_variant|||ENSG00000204147|ASAH2B|ENST00000374007||||-/160|protein_coding|1,upstream_gene_variant|||ENSG00000204147|ASAH2B|ENST00000483649|||||processed_transcript|1,upstream_gene_variant|||ENSG00000204147|ASAH2B|ENST00000374006||||-/165|protein_coding|1,upstream_gene_variant|||ENSG00000204147|ASAH2B|ENST00000185907||||-/160|protein_coding|1	GT:AD:DP:GQ:PL	./.	1/1:0,1:1:3.01:37,3,0	1/1:0,1:1:3.01:30,3,0	./.
chr10	126678092	.	G	A	89.08	.	AC=1;AF=0.13;AN=8;BaseQRankSum=-3.120;DP=185;Dels=0.00;FS=3.490;HRun=0;HaplotypeScore=3.3843;MQ=25.32;MQ0=0;MQRankSum=6.568;QD=2.02;ReadPosRankSum=-5.871;EFF=DOWNSTREAM(MODIFIER||||708|ZRANB1|protein_coding|CODING|ENST00000359653|),DOWNSTREAM(MODIFIER|||||CTBP2|processed_transcript|CODING|ENST00000395705|),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000337195|exon_10_126676421_126678267),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000411419|exon_10_126677794_126678267),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000494626|exon_10_126677794_126678267),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q445*|445|CTBP2|protein_coding|CODING|ENST00000531469|exon_10_126677794_126678267),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q513*|513|CTBP2|protein_coding|CODING|ENST00000334808|exon_10_126677704_126678267),STOP_GAINED(HIGH|NONSENSE|Caa/Taa|Q985*|985|CTBP2|protein_coding|CODING|ENST00000309035|exon_10_126677507_126678267);CSQ=stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000531469|11/11|||445/445|protein_coding|1,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000309035|9/9|||985/985|protein_coding|1,downstream_gene_variant|||ENSG00000019995|ZRANB1|ENST00000359653||||-/708|protein_coding|1,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000494626|11/11|||445/445|protein_coding|1,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000337195|11/11|||445/445|protein_coding|1,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000334808|9/9|||513/513|protein_coding|1,stop_gained|Caa/Taa|Q/*|ENSG00000175029|CTBP2|ENST00000411419|11/11|||445/445|protein_coding|1,downstream_gene_variant|||ENSG00000175029|CTBP2|ENST00000395705|||||processed_transcript|1	GT:AD:DP:GQ:PL	0/0:64,3:67:99:0,165,1505	0/0:11,1:12:7.31:0,7,240	0/0:52,10:62:54.97:0,55,1263	0/1:35,9:44:99:125,0,693
chr10	135210791	.	T	C	65.41	.	AC=4;AF=0.50;AN=8;BaseQRankSum=2.054;DP=11;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=0.2489;MQ=35.12;MQ0=0;MQRankSum=0.248;QD=16.35;ReadPosRankSum=-1.001;EFF=INTRON(MODIFIER||||226|MTG1.1|protein_coding|CODING|ENST00000537620|),INTRON(MODIFIER||||283|MTG1.1|protein_coding|CODING|ENST00000432508|),INTRON(MODIFIER||||334|MTG1.1|protein_coding|CODING|ENST00000317502|),INTRON(MODIFIER||||339|MTG1|protein_coding|CODING|ENST00000468317|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000460848|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000473735|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000477902|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000495014|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000498334|),INTRON(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000498790|),UPSTREAM(MODIFIER|||||MTG1.1|processed_transcript|CODING|ENST00000492266|);CSQ=intron_variant|||ENSG00000148824|MTG1|ENST00000317502||||-/334|protein_coding|1,upstream_gene_variant|||ENSG00000148824|MTG1|ENST00000492266|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000148824|MTG1|ENST00000460848|||||retained_intron|1,intron_variant|||ENSG00000254536|RP11-108K14.8|ENST00000468317||||-/339|protein_coding|1,intron_variant|||ENSG00000148824|MTG1|ENST00000477902||||-/293|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000148824|MTG1|ENST00000473735|||||retained_intron|1,intron_variant&nc_transcript_variant|||ENSG00000148824|MTG1|ENST00000498790|||||retained_intron|1,intron_variant|||ENSG00000148824|MTG1|ENST00000432508||||-/283|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000148824|MTG1|ENST00000495014|||||retained_intron|1	GT:AD:DP:GQ:PL	0/0:4,0:4:9:0,9,84	1/1:0,3:3:6.02:74,6,0	1/1:0,1:1:3.01:37,3,0	0/0:3,0:3:9.02:0,9,100
chr10	135336656	.	G	A	38.34	.	AC=4;AF=1.00;AN=4;DP=2;Dels=0.00;FS=0.000;HRun=4;HaplotypeScore=0.0000;MQ=37.00;MQ0=0;QD=19.17;EFF=INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),INTRON(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000463117|),INTRON(MODIFIER||||693|RP11-108K14.4.1|protein_coding|CODING|ENST00000356567|),INTRON(MODIFIER|||||RP11-108K14.4.1|retained_intron|CODING|ENST00000488261|),UPSTREAM(MODIFIER||||305|CYP2E1|protein_coding|CODING|ENST00000418356|),UPSTREAM(MODIFIER||||355|CYP2E1|protein_coding|CODING|ENST00000421586|),UPSTREAM(MODIFIER||||493|CYP2E1|protein_coding|CODING|ENST00000252945|),UPSTREAM(MODIFIER||||85|CYP2E1|protein_coding|CODING|ENST00000541261|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000477500|),UPSTREAM(MODIFIER|||||CYP2E1|processed_transcript|CODING|ENST00000480558|);CSQ=upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000418356||||-/306|protein_coding|1,intron_variant&nc_transcript_variant|||ENSG00000214279|RP11-108K14.4|ENST00000488261|||||retained_intron|1,intron_variant|||ENSG00000203772|SPRN|ENST00000541506||||-/151|protein_coding|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541261||||-/86|protein_coding|1,downstream_gene_variant|||ENSG00000268925|AL161645.2|ENST00000599428||||-/20|protein_coding|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000421586||||-/356|protein_coding|1,intron_variant|||ENSG00000130649|CYP2E1|ENST00000463117||||-/493|protein_coding|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000252945||||-/493|protein_coding|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000541080||||-/43|nonsense_mediated_decay|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000477500|||||processed_transcript|1,upstream_gene_variant|||ENSG00000130649|CYP2E1|ENST00000480558|||||processed_transcript|1,intron_variant&nc_transcript_variant|||ENSG00000214279|RP11-108K14.4|ENST00000356567|||||unitary_pseudogene|1	GT:AD:DP:GQ:PL	./.	1/1:0,1:1:3.01:37,3,0	./.	1/1:0,1:1:3.01:34,3,0
chr10	135369532	.	T	C	122.62	.	AC=2;AF=0.25;AN=8;BaseQRankSum=2.118;DP=239;Dels=0.00;FS=5.194;HRun=2;HaplotypeScore=5.7141;MQ=36.02;MQ0=0;MQRankSum=0.082;QD=2.31;ReadPosRankSum=-0.695;EFF=DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000460441|),DOWNSTREAM(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000482127|),EXON(MODIFIER|||||CYP2E1|retained_intron|CODING|ENST00000368520|),EXON(MODIFIER|||||SYCE1|processed_transcript|CODING|ENST00000479535|),INTRON(MODIFIER||||151|SPRN|protein_coding|CODING|ENST00000541506|),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000368517|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K147R|282|SYCE1|protein_coding|CODING|ENST00000432597|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|318|SYCE1|protein_coding|CODING|ENST00000303903|exon_10_135369485_135369551),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aAg/aGg|K183R|351|SYCE1|protein_coding|CODING|ENST00000343131|exon_10_135369485_135369551);CSQ=missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000303903|9/13|benign(0.001)|tolerated(1)|183/318|protein_coding|1,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000432597|10/14|benign(0.001)|tolerated(1)|147/282|protein_coding|1,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000343131|9/13|benign(0.002)|tolerated(1)|183/351|protein_coding|1,intron_variant|||ENSG00000203772|SPRN|ENST00000541506||||-/151|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000130649|CYP2E1|ENST00000368520|6/6||||retained_intron|1,missense_variant|aAg/aGg|K/R|ENSG00000171772|SYCE1|ENST00000368517|9/13|benign(0.001)|tolerated(1)|147/282|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000171772|SYCE1|ENST00000479535|7/11||||retained_intron|1	GT:AD:DP:GQ:PL	0/0:40,0:40:63.06:0,63,628	0/1:27,5:32:49.03:49,0,658	0/1:15,5:21:99:115,0,261	0/0:145,0:146:99:0,319,3399
chr16	72057435	.	C	T	572.98	.	AC=1;AF=0.13;AN=8;BaseQRankSum=-2.270;DP=260;Dels=0.00;FS=0.000;HRun=0;HaplotypeScore=4.5319;MQ=36.53;MQ0=0;MQRankSum=0.596;QD=8.07;ReadPosRankSum=0.927;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cgg/Tgg|R346W|395|DHODH|protein_coding|CODING|ENST00000219240|exon_16_72057373_72057532);CSQ=missense_variant|Cgg/Tgg|R/W|ENSG00000102967|DHODH|ENST00000219240|8/9|probably_damaging(0.956)|deleterious(0)|346/395|protein_coding|1,non_coding_exon_variant&nc_transcript_variant|||ENSG00000102967|DHODH|ENST00000571392|3/4||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000572003|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573843|||||retained_intron|1,downstream_gene_variant|||ENSG00000102967|DHODH|ENST00000573922|||||processed_transcript|1,intron_variant|||ENSG00000102967|DHODH|ENST00000574309||||-/193|protein_coding|1,missense_variant|Cgg/Tgg|R/W|ENSG00000102967|DHODH|ENST00000572887|8/9|probably_damaging(0.946)|deleterious(0)|344/393|protein_coding|1	GT:AD:DP:GQ:PL	0/1:37,33:71:99:609,0,666	0/0:56,0:56:99:0,135,1543	0/0:67,1:68:99:0,120,1460	0/0:65,0:65:99:0,180,1982