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##fileformat=VCFv4.1
##source=pseq
##INFO=<ID=AC,Number=-1,Type=Integer,Description="Allele count for each alternate allele">
##INFO=<ID=AF,Number=-1,Type=Float,Description="Frequency for each alternate allele (estimated from primary data, not called genotypes)">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=DB,Number=1,Type=Integer,Description="dbSNP membership">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Combined depth across samples">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS mapping quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Number of MQ == 0 reads covering this record">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##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=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=MLEAC,Number=-1,Type=Integer,Description="Maximum likelihood expectation (MLE) for the allele counts (not necessarily the same as the AC), for each ALT allele, in the same order as listed">
##INFO=<ID=MLEAF,Number=-1,Type=Float,Description="Maximum likelihood expectation (MLE) for the allele frequency (not necessarily the same as the AF), for each ALT allele, in the same order as listed">
##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=RPA,Number=-1,Type=Integer,Description="Number of times tandem repeat unit is repeated, for each allele (including reference)">
##INFO=<ID=RU,Number=1,Type=String,Description="Tandem repeat unit (bases)">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=STR,Number=0,Type=Flag,Description="Variant is a short tandem repeat">
##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds ratio of being a true variant versus being false under the trained gaussian mixture model">
##INFO=<ID=culprit,Number=1,Type=String,Description="The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out">
##INFO=<ID=ANC,Number=1,Type=String,Description="ancestral state from ensemble">
##INFO=<ID=REFisANC,Number=1,Type=String,Description="whether the reference allele is the ancestral">
##INFO=<ID=EFF,Number=-1,Type=String,Description="Predicted effects for this variant.Format: 'Effect ( Effect_Impact | Functional_Class | Codon_Change | Amino_Acid_change| Amino_Acid_length | Gene_Name | Transcript_BioType | Gene_Coding | Transcript_ID | Exon | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="phred-scaled genotype likelihoods; for AA,AB,BB where A=ref, B=alt">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="phred-scaled genotype quality, -10log_10p(genotype call is wrong)">
##FORMAT=<ID=AD,Number=-1,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FILTER=<ID=PASS,Description="Passed variant FILTERs">
##FILTER=<ID=LowQual,Description="Low quality">
##FILTER=<ID=VQSRTrancheSNP99.00to99.90,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -1.7803 <= x < 2.3186">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -13304.4066">
##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -13304.4066 <= x < -1.7803">
##SnpEffVersion="3.3h (build 2013-08-20), by Pablo Cingolani"
##SnpEffCmd="SnpEff -lof GRCh37.68 /home/data/temp/evan/SA_exomes_callableANC.RefAnc.SNPEff_EvansIndivs.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 | Transcript_BioType | Gene_Coding | Transcript_ID | Exon | GenotypeNum [ | ERRORS | WARNINGS ] )' ">
##INFO=<ID=LOF,Number=.,Type=String,Description="Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
##INFO=<ID=NMD,Number=.,Type=String,Description="Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | Number_of_transcripts_in_gene | Percent_of_transcripts_affected' ">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SA1025 SA006 SA008 SA011 SA012 SA035 SA051 SA052 SA054 SA1000 SA1001 SA1002 SA1006 SA1010 SA1011
chr1 1219382 rs114582555 C G 156.61 PASS AC=1;AF=0.008475;AN=118;DP=197;MQ=55.83;MQ0=0;BaseQRankSum=2.15;Dels=0;FS=3.435;HaplotypeScore=0.4738;InbreedingCoeff=-0.1164;MLEAC=1;MLEAF=0.008475;MQRankSum=2.556;QD=17.4;ReadPosRankSum=0.952;VQSLOD=2.87;culprit=InbreedingCoeff;ANC=c;REFisANC=true;EFF=DOWNSTREAM(MODIFIER||3582|||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139||1),DOWNSTREAM(MODIFIER||4609|||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732||1),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5|1),EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q126E|802|SCNN1D|protein_coding|CODING|ENST00000379116|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q28E|704|SCNN1D|protein_coding|CODING|ENST00000325425|2|1),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3|1),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2|1),START_GAINED(LOW||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6|1),STOP_GAINED(HIGH|NONSENSE|tCa/tGa|S29*|138|SCNN1D|protein_coding|CODING|ENST00000470022|3|1),UPSTREAM(MODIFIER||3107||306|SCNN1D|protein_coding|CODING|ENST00000379099||1);EFF=DOWNSTREAM(MODIFIER||3582|||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000434139||1),DOWNSTREAM(MODIFIER||4609|||RP5-902P8.10|processed_transcript|NON_CODING|ENST00000453732||1),EXON(MODIFIER|||||SCNN1D|nonsense_mediated_decay|CODING|ENST00000379101|5|1),EXON(MODIFIER|||||SCNN1D|processed_transcript|CODING|ENST00000467651|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q126E|802|SCNN1D|protein_coding|CODING|ENST00000379116|5|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q28E|704|SCNN1D|protein_coding|CODING|ENST00000325425|2|1),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000338555|3|1),START_GAINED(LOW||||638|SCNN1D|protein_coding|CODING|ENST00000400928|2|1),START_GAINED(LOW||||669|SCNN1D|protein_coding|CODING|ENST00000379110|6|1),STOP_GAINED(HIGH|NONSENSE|tCa/tGa|S29*|138|SCNN1D|protein_coding|CODING|ENST00000470022|3|1),UPSTREAM(MODIFIER||3107||306|SCNN1D|protein_coding|CODING|ENST00000379099||1);LOF=(SCNN1D|ENSG00000162572|9|0.11);NMD=(SCNN1D|ENSG00000162572|9|0.11) GT:AD:DP:GQ:PL 0/0:4,0:4:12:0,12,142 0/0:2,0:2:6:0,6,61 .:.:.:.:. 0/0:2,0:2:6:0,6,79 0/0:4,0:4:12:0,12,138 0/0:2,0:2:6:0,6,71 .:.:.:.:. 0/0:7,0:7:21:0,21,275 0/0:3,0:3:9:0,9,110 0/0:1,0:1:3:0,3,37 0/0:3,1:4:6:0,6,83 0/0:4,0:4:9:0,9,113 .:.:.:.:. .:.:.:.:. 0/0:1,0:1:3:0,3,33
chr1 1558792 rs12755088 T C 10073.4 PASS AC=108;AF=0.659;AN=164;DP=653;MQ=55.8;MQ0=0;BaseQRankSum=-0.772;Dels=0;FS=3.546;HaplotypeScore=0.648;InbreedingCoeff=0.1261;MLEAC=105;MLEAF=0.64;MQRankSum=1.044;QD=19.08;ReadPosRankSum=0.452;VQSLOD=4.35;culprit=HaplotypeScore;ANC=T;REFisANC=true;EFF=DOWNSTREAM(MODIFIER||4202|||MIB2|retained_intron|CODING|ENST00000477990||1),EXON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000487053|3|1),EXON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000489635|3|1),EXON(MODIFIER|||||MIB2|processed_transcript|CODING|ENST00000512004|1|1),EXON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000507229|2|1),EXON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000511502|3|1),INTRON(MODIFIER||||1056|MIB2|protein_coding|CODING|ENST00000355826|2|1),INTRON(MODIFIER||||147|MIB2|protein_coding|CODING|ENST00000503789|1|1),INTRON(MODIFIER||||174|MIB2|protein_coding|CODING|ENST00000510793|1|1),INTRON(MODIFIER||||753|MIB2|protein_coding|CODING|ENST00000378712|2|1),INTRON(MODIFIER||||919|MIB2|protein_coding|CODING|ENST00000378708|1|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000502470|2|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000506488|1|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000514363|2|1),INTRON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000479659|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1005|MIB2|protein_coding|CODING|ENST00000518681|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1066|MIB2|protein_coding|CODING|ENST00000520777|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1070|MIB2|protein_coding|CODING|ENST00000505820|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|1013|MIB2|protein_coding|CODING|ENST00000357210|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|977|MIB2|protein_coding|CODING|ENST00000378710|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|978|MIB2|protein_coding|CODING|ENST00000360522|3|1),START_LOST(HIGH|MISSENSE|aTg/aCg|M1T|969|MIB2|protein_coding|CODING|ENST00000504599|2|1),UPSTREAM(MODIFIER||1332|||MIB2|retained_intron|CODING|ENST00000467597||1),UPSTREAM(MODIFIER||1675|||MIB2|retained_intron|CODING|ENST00000508148||1),UPSTREAM(MODIFIER||169|||MIB2|retained_intron|CODING|ENST00000508455||1),UPSTREAM(MODIFIER||2155|||MIB2|nonsense_mediated_decay|CODING|ENST00000486072||1),UPSTREAM(MODIFIER||3448|||MIB2|retained_intron|CODING|ENST00000505370||1),UPSTREAM(MODIFIER||390||828|MIB2|protein_coding|CODING|ENST00000514234||1),UPSTREAM(MODIFIER||4048|||MIB2|retained_intron|CODING|ENST00000473511||1),UPSTREAM(MODIFIER||4110|||MIB2|retained_intron|CODING|ENST00000464570||1);EFF=DOWNSTREAM(MODIFIER||4202|||MIB2|retained_intron|CODING|ENST00000477990||1),EXON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000487053|3|1),EXON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000489635|3|1),EXON(MODIFIER|||||MIB2|processed_transcript|CODING|ENST00000512004|1|1),EXON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000507229|2|1),EXON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000511502|3|1),INTRON(MODIFIER||||1056|MIB2|protein_coding|CODING|ENST00000355826|2|1),INTRON(MODIFIER||||147|MIB2|protein_coding|CODING|ENST00000503789|1|1),INTRON(MODIFIER||||174|MIB2|protein_coding|CODING|ENST00000510793|1|1),INTRON(MODIFIER||||753|MIB2|protein_coding|CODING|ENST00000378712|2|1),INTRON(MODIFIER||||919|MIB2|protein_coding|CODING|ENST00000378708|1|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000502470|2|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000506488|1|1),INTRON(MODIFIER|||||MIB2|nonsense_mediated_decay|CODING|ENST00000514363|2|1),INTRON(MODIFIER|||||MIB2|retained_intron|CODING|ENST00000479659|2|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1005|MIB2|protein_coding|CODING|ENST00000518681|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1066|MIB2|protein_coding|CODING|ENST00000520777|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M102T|1070|MIB2|protein_coding|CODING|ENST00000505820|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|1013|MIB2|protein_coding|CODING|ENST00000357210|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|977|MIB2|protein_coding|CODING|ENST00000378710|3|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|aTg/aCg|M45T|978|MIB2|protein_coding|CODING|ENST00000360522|3|1),START_LOST(HIGH|MISSENSE|aTg/aCg|M1T|969|MIB2|protein_coding|CODING|ENST00000504599|2|1),UPSTREAM(MODIFIER||1332|||MIB2|retained_intron|CODING|ENST00000467597||1),UPSTREAM(MODIFIER||1675|||MIB2|retained_intron|CODING|ENST00000508148||1),UPSTREAM(MODIFIER||169|||MIB2|retained_intron|CODING|ENST00000508455||1),UPSTREAM(MODIFIER||2155|||MIB2|nonsense_mediated_decay|CODING|ENST00000486072||1),UPSTREAM(MODIFIER||3448|||MIB2|retained_intron|CODING|ENST00000505370||1),UPSTREAM(MODIFIER||390||828|MIB2|protein_coding|CODING|ENST00000514234||1),UPSTREAM(MODIFIER||4048|||MIB2|retained_intron|CODING|ENST00000473511||1),UPSTREAM(MODIFIER||4110|||MIB2|retained_intron|CODING|ENST00000464570||1);LOF=(MIB2|ENSG00000197530|35|0.03) GT:AD:DP:GQ:PL 1/1:0,7:7:12:157,12,0 0/0:7,0:7:18:0,18,166 1/1:0,4:4:12:142,12,0 0/1:14,11:24:99:277,0,369 0/1:12,17:28:99:427,0,258 0/0:16,0:16:42:0,42,450 1/1:0,38:38:96:1067,96,0 0/0:20,0:20:51:0,51,599 0/1:9,14:22:99:278,0,123 1/1:0,5:5:12:136,12,0 0/0:3,1:4:6:0,6,82 1/1:0,4:4:9:95,9,0 1/1:0,4:4:12:139,12,0 1/1:0,2:2:3:30,3,0 .:.:.:.:.
chr1 5935162 rs1287637 A T 31049.1 PASS AC=157;AF=0.913;AN=172;DP=1122;MQ=57.11;MQ0=0;BaseQRankSum=-7.118;Dels=0;FS=2.93;HaplotypeScore=0.4626;InbreedingCoeff=-0.1035;MLEAC=156;MLEAF=0.907;MQRankSum=0.657;QD=27.67;ReadPosRankSum=1.549;VQSLOD=3.46;culprit=InbreedingCoeff;ANC=t;REFisANC=false;EFF=DOWNSTREAM(MODIFIER||1777|||NPHP4|retained_intron|CODING|ENST00000470763||1),INTRON(MODIFIER||||1426|NPHP4|protein_coding|CODING|ENST00000378156|20|1),INTRON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|17|1),INTRON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|23|1),INTRON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|16|1),INTRON(MODIFIER|||||NPHP4|retained_intron|CODING|ENST00000506941|1|1),SPLICE_SITE_ACCEPTOR(HIGH||||1426|NPHP4|protein_coding|CODING|ENST00000378156|21|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|18|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|24|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|processed_transcript|CODING|ENST00000478423|17|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|retained_intron|CODING|ENST00000506941|2|1),UPSTREAM(MODIFIER||1261|||NPHP4|retained_intron|CODING|ENST00000468253||1);EFF=DOWNSTREAM(MODIFIER||1777|||NPHP4|ambiguous_orf|CODING|ENST00000470763||1),INTRON(MODIFIER||||1426|NPHP4|protein_coding|CODING|ENST00000378156|20|1),INTRON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|17|1),INTRON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|23|1),INTRON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|16|1),INTRON(MODIFIER|||||NPHP4|retained_intron|CODING|ENST00000506941|1|1),SPLICE_SITE_ACCEPTOR(HIGH||||1426|NPHP4|protein_coding|CODING|ENST00000378156|21|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|18|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|24|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|processed_transcript|CODING|ENST00000478423|17|1),SPLICE_SITE_ACCEPTOR(HIGH|||||NPHP4|retained_intron|CODING|ENST00000506941|2|1),UPSTREAM(MODIFIER||1261|||NPHP4|retained_intron|CODING|ENST00000468253||1);LOF=(NPHP4|ENSG00000131697|10|0.10) GT:AD:DP:GQ:PL 1/1:0,10:10:21:243,21,0 1/1:0,9:10:27:280,27,0 0/1:2,4:6:53:126,0,53 0/1:13,14:26:99:401,0,369 1/1:0,35:35:99:1219,102,0 1/1:0,43:43:99:1400,126,0 1/1:0,82:82:99:2816,244,0 1/1:0,34:34:99:1215,102,0 0/1:25,28:51:99:694,0,731 1/1:0,7:8:21:216,21,0 1/1:0,10:10:27:312,27,0 1/1:0,7:7:15:185,15,0 1/1:0,4:4:12:137,12,0 1/1:0,7:7:15:171,15,0 1/1:0,5:5:15:178,15,0
chr1 5965750 rs113413307 G A,C 13827.0 PASS AC=2,40;AF=0.012,0.233;AN=172;DP=2212;MQ=57.53;MQ0=0;BaseQRankSum=4.389;Dels=0;FS=0.82;HaplotypeScore=2.4543;InbreedingCoeff=-0.026;MLEAC=2,40;MLEAF=0.012,0.233;MQRankSum=0.621;QD=14.62;ReadPosRankSum=2.276;VQSLOD=3.48;culprit=HaplotypeScore;ANC=G;REFisANC=true;EFF=EXON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|14|1),EXON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|14|2),EXON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|10|1),EXON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|10|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q569E|1426|NPHP4|protein_coding|CODING|ENST00000378156|14|2),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q569*|1426|NPHP4|protein_coding|CODING|ENST00000378156|14|1),UPSTREAM(MODIFIER||366|||NPHP4|nonsense_mediated_decay|CODING|ENST00000466897||1),UPSTREAM(MODIFIER||366|||NPHP4|nonsense_mediated_decay|CODING|ENST00000466897||2),UTR_3_PRIME(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|11|1),UTR_3_PRIME(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|11|2);EFF=EXON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|14|1),EXON(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000489180|14|2),EXON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|10|1),EXON(MODIFIER|||||NPHP4|processed_transcript|CODING|ENST00000478423|10|2),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Cag/Gag|Q569E|1426|NPHP4|protein_coding|CODING|ENST00000378156|14|2),STOP_GAINED(HIGH|NONSENSE|Cag/Tag|Q569*|1426|NPHP4|protein_coding|CODING|ENST00000378156|14|1),UPSTREAM(MODIFIER||366|||NPHP4|nonsense_mediated_decay|CODING|ENST00000466897||1),UPSTREAM(MODIFIER||366|||NPHP4|nonsense_mediated_decay|CODING|ENST00000466897||2),UTR_3_PRIME(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|11|1),UTR_3_PRIME(MODIFIER|||||NPHP4|nonsense_mediated_decay|CODING|ENST00000378169|11|2);LOF=(NPHP4|ENSG00000131697|10|0.10);NMD=(NPHP4|ENSG00000131697|10|0.10) GT:AD:DP:GQ:PL 0/2:15,0,10:25:99:342,373,751,0,379,348 0/0:21,0,0:21:42:0,42,418,42,418,418 0/0:33,0,0:33:78:0,78,989,78,989,989 0/0:48,0,1:48:87:0,87,1093,87,1093,1093 0/0:50,1,0:50:93:0,93,1173,93,1173,1173 0/0:26,0,0:26:60:0,60,655,60,655,655 0/2:24,0,30:53:99:692,761,1507,0,745,676 0/2:28,0,30:56:99:600,666,1400,0,734,677 0/0:53,0,1:54:99:0,108,1318,108,1318,1318 0/2:9,0,7:16:99:173,194,435,0,241,223 0/0:19,0,0:19:42:0,42,522,42,522,522 0/0:21,0,1:21:54:0,54,599,54,599,599 0/0:15,0,0:15:36:0,36,404,36,404,404 0/0:12,0,1:14:27:0,27,318,27,318,318 0/0:13,0,0:13:21:0,21,242,21,242,242
chr1 6522724 rs145286562 C T 2029.95 PASS AC=2;AF=0.012;AN=172;DP=5417;MQ=58.19;MQ0=0;BaseQRankSum=-11.642;Dels=0;FS=4.025;HaplotypeScore=2.4394;InbreedingCoeff=-0.0118;MLEAC=2;MLEAF=0.012;MQRankSum=1.326;QD=11.4;ReadPosRankSum=1.075;VQSLOD=3.17;culprit=HaplotypeScore;ANC=C;REFisANC=true;EFF=DOWNSTREAM(MODIFIER||1294||187|ESPN|protein_coding|CODING|ENST00000434576||1),DOWNSTREAM(MODIFIER||1294|||ESPN|processed_transcript|CODING|ENST00000468561||1),DOWNSTREAM(MODIFIER||1447|||TNFRSF25|retained_intron|CODING|ENST00000453341||1),DOWNSTREAM(MODIFIER||1720||288|ESPN|protein_coding|CODING|ENST00000416731||1),DOWNSTREAM(MODIFIER||1720||854|ESPN|protein_coding|CODING|ENST00000377828||1),DOWNSTREAM(MODIFIER||1735||288|ESPN|protein_coding|CODING|ENST00000461727||1),DOWNSTREAM(MODIFIER||1903|||TNFRSF25|retained_intron|CODING|ENST00000515145||1),DOWNSTREAM(MODIFIER||2253|||ESPN|retained_intron|CODING|ENST00000477679||1),DOWNSTREAM(MODIFIER||2612|||ESPN|processed_transcript|CODING|ENST00000475228||1),DOWNSTREAM(MODIFIER||3428||1006|PLEKHG5|protein_coding|CODING|ENST00000340850||1),DOWNSTREAM(MODIFIER||3428||1006|PLEKHG5|protein_coding|CODING|ENST00000400913||1),DOWNSTREAM(MODIFIER||3428||1083|PLEKHG5|protein_coding|CODING|ENST00000377748||1),DOWNSTREAM(MODIFIER||3428|||PLEKHG5|retained_intron|CODING|ENST00000489097||1),DOWNSTREAM(MODIFIER||4458||1006|PLEKHG5|protein_coding|CODING|ENST00000377728||1),DOWNSTREAM(MODIFIER||4458||1043|PLEKHG5|protein_coding|CODING|ENST00000377732||1),DOWNSTREAM(MODIFIER||4458||1062|PLEKHG5|protein_coding|CODING|ENST00000400915||1),DOWNSTREAM(MODIFIER||4458||852|PLEKHG5|protein_coding|CODING|ENST00000377740||1),DOWNSTREAM(MODIFIER||4458||912|PLEKHG5|protein_coding|CODING|ENST00000491384||1),DOWNSTREAM(MODIFIER||4458||930|PLEKHG5|protein_coding|CODING|ENST00000377725||1),DOWNSTREAM(MODIFIER||4458|||PLEKHG5|retained_intron|CODING|ENST00000487949||1),DOWNSTREAM(MODIFIER||4459||1006|PLEKHG5|protein_coding|CODING|ENST00000377737||1),DOWNSTREAM(MODIFIER||4459||1075|PLEKHG5|protein_coding|CODING|ENST00000535355||1),DOWNSTREAM(MODIFIER||4841||1085|PLEKHG5|protein_coding|CODING|ENST00000537245||1),DOWNSTREAM(MODIFIER||872|||TNFRSF25|processed_transcript|CODING|ENST00000461703||1),EXON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000414040|7|1),EXON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000485036|7|1),EXON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000469691|6|1),EXON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000473343|2|1),EXON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000513135|4|1),INTRON(MODIFIER||||234|TNFRSF25|protein_coding|CODING|ENST00000351748|2|1),INTRON(MODIFIER||||380|TNFRSF25|protein_coding|CODING|ENST00000351959|6|1),INTRON(MODIFIER||||44|TNFRSF25|protein_coding|CODING|ENST00000481401|6|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502588|4|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502730|3|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000510563|5|1),INTRON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000453260|1|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D192N|372|TNFRSF25|protein_coding|CODING|ENST00000348333|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D237N|417|TNFRSF25|protein_coding|CODING|ENST00000356876|8|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D246N|426|TNFRSF25|protein_coding|CODING|ENST00000377782|8|1),SPLICE_SITE_ACCEPTOR(HIGH||||234|TNFRSF25|protein_coding|CODING|ENST00000351748|3|1),SPLICE_SITE_ACCEPTOR(HIGH||||380|TNFRSF25|protein_coding|CODING|ENST00000351959|7|1),SPLICE_SITE_ACCEPTOR(HIGH||||44|TNFRSF25|protein_coding|CODING|ENST00000481401|7|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502588|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000510563|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|retained_intron|CODING|ENST00000453260|2|1),UPSTREAM(MODIFIER||57|||TNFRSF25|processed_transcript|CODING|ENST00000475730||1),UTR_3_PRIME(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000480393|7|1);EFF=DOWNSTREAM(MODIFIER||1294||187|ESPN|protein_coding|CODING|ENST00000434576||1),DOWNSTREAM(MODIFIER||1294|||ESPN|processed_transcript|CODING|ENST00000468561||1),DOWNSTREAM(MODIFIER||1447|||TNFRSF25|retained_intron|CODING|ENST00000453341||1),DOWNSTREAM(MODIFIER||1720||288|ESPN|protein_coding|CODING|ENST00000416731||1),DOWNSTREAM(MODIFIER||1720||854|ESPN|protein_coding|CODING|ENST00000377828||1),DOWNSTREAM(MODIFIER||1735|||ESPN|processed_transcript|CODING|ENST00000461727||1),DOWNSTREAM(MODIFIER||1903|||TNFRSF25|retained_intron|CODING|ENST00000515145||1),DOWNSTREAM(MODIFIER||2253|||ESPN|processed_transcript|CODING|ENST00000477679||1),DOWNSTREAM(MODIFIER||2612|||ESPN|processed_transcript|CODING|ENST00000475228||1),DOWNSTREAM(MODIFIER||3428||1006|PLEKHG5|protein_coding|CODING|ENST00000340850||1),DOWNSTREAM(MODIFIER||3428||1006|PLEKHG5|protein_coding|CODING|ENST00000400913||1),DOWNSTREAM(MODIFIER||3428||1083|PLEKHG5|protein_coding|CODING|ENST00000377748||1),DOWNSTREAM(MODIFIER||3428|||PLEKHG5|processed_transcript|CODING|ENST00000489097||1),DOWNSTREAM(MODIFIER||4458||1006|PLEKHG5|protein_coding|CODING|ENST00000377728||1),DOWNSTREAM(MODIFIER||4458||1043|PLEKHG5|protein_coding|CODING|ENST00000377732||1),DOWNSTREAM(MODIFIER||4458||1062|PLEKHG5|protein_coding|CODING|ENST00000400915||1),DOWNSTREAM(MODIFIER||4458||852|PLEKHG5|protein_coding|CODING|ENST00000377740||1),DOWNSTREAM(MODIFIER||4458||930|PLEKHG5|protein_coding|CODING|ENST00000377725||1),DOWNSTREAM(MODIFIER||4458|||PLEKHG5|processed_transcript|CODING|ENST00000487949||1),DOWNSTREAM(MODIFIER||4458|||PLEKHG5|processed_transcript|CODING|ENST00000491384||1),DOWNSTREAM(MODIFIER||4459||1006|PLEKHG5|protein_coding|CODING|ENST00000377737||1),DOWNSTREAM(MODIFIER||4459||1075|PLEKHG5|protein_coding|CODING|ENST00000535355||1),DOWNSTREAM(MODIFIER||4841||1085|PLEKHG5|protein_coding|CODING|ENST00000537245||1),DOWNSTREAM(MODIFIER||872|||TNFRSF25|processed_transcript|CODING|ENST00000461703||1),EXON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000414040|7|1),EXON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000485036|7|1),EXON(MODIFIER|||||TNFRSF25|processed_transcript|CODING|ENST00000469691|6|1),EXON(MODIFIER|||||TNFRSF25|processed_transcript|CODING|ENST00000473343|2|1),EXON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000513135|4|1),INTRON(MODIFIER||||234|TNFRSF25|protein_coding|CODING|ENST00000351748|2|1),INTRON(MODIFIER||||380|TNFRSF25|protein_coding|CODING|ENST00000351959|6|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502588|4|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502730|3|1),INTRON(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000510563|5|1),INTRON(MODIFIER|||||TNFRSF25|processed_transcript|CODING|ENST00000481401|6|1),INTRON(MODIFIER|||||TNFRSF25|retained_intron|CODING|ENST00000453260|1|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D192N|372|TNFRSF25|protein_coding|CODING|ENST00000348333|7|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D237N|417|TNFRSF25|protein_coding|CODING|ENST00000356876|8|1),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Gat/Aat|D246N|426|TNFRSF25|protein_coding|CODING|ENST00000377782|8|1),SPLICE_SITE_ACCEPTOR(HIGH||||234|TNFRSF25|protein_coding|CODING|ENST00000351748|3|1),SPLICE_SITE_ACCEPTOR(HIGH||||380|TNFRSF25|protein_coding|CODING|ENST00000351959|7|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000502588|5|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000510563|6|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|processed_transcript|CODING|ENST00000481401|7|1),SPLICE_SITE_ACCEPTOR(HIGH|||||TNFRSF25|retained_intron|CODING|ENST00000453260|2|1),UPSTREAM(MODIFIER||57|||TNFRSF25|processed_transcript|CODING|ENST00000475730||1),UTR_3_PRIME(MODIFIER|||||TNFRSF25|nonsense_mediated_decay|CODING|ENST00000480393|7|1);LOF=(TNFRSF25|ENSG00000215788|20|0.10) GT:AD:DP:GQ:PL 0/0:56,0:56:99:0,138,1868 0/0:26,0:26:78:0,78,770 0/0:54,0:54:99:0,141,1818 0/0:84,0:84:99:0,238,3087 0/0:92,0:92:99:0,250,3262 0/0:52,0:52:99:0,132,1586 0/0:111,0:111:99:0,292,3612 0/0:102,0:102:99:0,241,3181 0/0:81,0:81:99:0,223,2842 0/0:55,0:55:99:0,135,1640 0/0:61,0:61:99:0,150,1849 0/0:58,0:58:99:0,138,1683 0/0:32,0:32:81:0,81,987 0/0:38,0:38:90:0,90,1134 0/0:31,0:31:66:0,66,809
chr1 7806143 . A T 776.27 PASS AC=1;AF=0.005814;AN=172;DP=7158;MQ=58.38;MQ0=0;BaseQRankSum=-6.456;Dels=0;FS=4.201;HaplotypeScore=4.4841;InbreedingCoeff=-0.0065;MLEAC=1;MLEAF=0.005814;MQRankSum=0.79;QD=8.44;ReadPosRankSum=0.099;VQSLOD=3.1;culprit=QD;ANC=A;REFisANC=true;EFF=STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K101*|237|CAMTA1|protein_coding|CODING|ENST00000476864|2|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K102*|238|CAMTA1|protein_coding|CODING|ENST00000490905|2|1|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K1523*|1659|CAMTA1|protein_coding|CODING|ENST00000439411|18|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K1537*|1673|CAMTA1|protein_coding|CODING|ENST00000303635|18|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K493*|636|CAMTA1|protein_coding|CODING|ENST00000495233|6|1);EFF=STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K101*|237|CAMTA1|protein_coding|CODING|ENST00000476864|2|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K102*|238|CAMTA1|protein_coding|CODING|ENST00000490905|2|1|WARNING_TRANSCRIPT_NO_START_CODON),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K1523*|1659|CAMTA1|protein_coding|CODING|ENST00000439411|18|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K1537*|1673|CAMTA1|protein_coding|CODING|ENST00000303635|18|1),STOP_GAINED(HIGH|NONSENSE|Aaa/Taa|K493*|636|CAMTA1|protein_coding|CODING|ENST00000495233|6|1);LOF=(CAMTA1|ENSG00000171735|17|0.29);NMD=(CAMTA1|ENSG00000171735|17|0.29) GT:AD:DP:GQ:PL 0/0:79,1:77:99:0,187,2420 0/0:4,0:4:12:0,12,125 0/0:128,0:128:99:0,334,4150 0/0:23,0:23:66:0,66,811 0/0:34,0:34:99:0,99,1239 0/0:4,0:4:12:0,12,137 0/0:15,0:15:39:0,39,467 0/0:20,0:20:60:0,60,736 0/0:29,0:29:84:0,84,1030 0/0:47,0:47:99:0,126,1502 0/0:79,0:79:99:0,196,2333 0/0:91,0:91:99:0,229,2767 0/0:83,0:83:99:0,205,2510 0/0:133,0:133:99:0,301,3764 0/0:66,0:65:99:0,159,1950
|
