Mercurial > repos > waqas > macaron
view MACARON-GenMed-LabEx/demo/variants_of_interest.vcf @ 0:c9636a827049 draft default tip
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| author | waqas |
|---|---|
| date | Wed, 12 Sep 2018 08:45:03 -0400 |
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##fileformat=VCFv4.2 ##ALT=<ID=NON_REF,Description="Represents any possible alternative allele at this location"> ##FILTER=<ID=LowQual,Description="Low quality"> ##FILTER=<ID=VQSRTrancheINDEL99.00to99.90,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -16.0255 <= x < -0.8001"> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00+,Description="Truth sensitivity tranche level for INDEL model at VQS Lod < -37813.1681"> ##FILTER=<ID=VQSRTrancheINDEL99.90to100.00,Description="Truth sensitivity tranche level for INDEL model at VQS Lod: -37813.1681 <= x < -16.0255"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00+,Description="Truth sensitivity tranche level for SNP model at VQS Lod < -123623.5614"> ##FILTER=<ID=VQSRTrancheSNP99.90to100.00,Description="Truth sensitivity tranche level for SNP model at VQS Lod: -123623.5614 <= x < -2.5203"> ##FORMAT=<ID=AD,Number=R,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=Integer,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum DP observed within the GVCF block"> ##FORMAT=<ID=PGT,Number=1,Type=String,Description="Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another"> ##FORMAT=<ID=PID,Number=1,Type=String,Description="Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> ##FORMAT=<ID=RGQ,Number=1,Type=Integer,Description="Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong)"> ##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias."> ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) ##GVCFBlock11-12=minGQ=11(inclusive),maxGQ=12(exclusive) ##GVCFBlock12-13=minGQ=12(inclusive),maxGQ=13(exclusive) ##GVCFBlock13-14=minGQ=13(inclusive),maxGQ=14(exclusive) ##GVCFBlock14-15=minGQ=14(inclusive),maxGQ=15(exclusive) ##GVCFBlock15-16=minGQ=15(inclusive),maxGQ=16(exclusive) ##GVCFBlock16-17=minGQ=16(inclusive),maxGQ=17(exclusive) ##GVCFBlock17-18=minGQ=17(inclusive),maxGQ=18(exclusive) ##GVCFBlock18-19=minGQ=18(inclusive),maxGQ=19(exclusive) ##GVCFBlock19-20=minGQ=19(inclusive),maxGQ=20(exclusive) ##GVCFBlock2-3=minGQ=2(inclusive),maxGQ=3(exclusive) ##GVCFBlock20-21=minGQ=20(inclusive),maxGQ=21(exclusive) ##GVCFBlock21-22=minGQ=21(inclusive),maxGQ=22(exclusive) ##GVCFBlock22-23=minGQ=22(inclusive),maxGQ=23(exclusive) ##GVCFBlock23-24=minGQ=23(inclusive),maxGQ=24(exclusive) ##GVCFBlock24-25=minGQ=24(inclusive),maxGQ=25(exclusive) ##GVCFBlock25-26=minGQ=25(inclusive),maxGQ=26(exclusive) ##GVCFBlock26-27=minGQ=26(inclusive),maxGQ=27(exclusive) ##GVCFBlock27-28=minGQ=27(inclusive),maxGQ=28(exclusive) ##GVCFBlock28-29=minGQ=28(inclusive),maxGQ=29(exclusive) ##GVCFBlock29-30=minGQ=29(inclusive),maxGQ=30(exclusive) ##GVCFBlock3-4=minGQ=3(inclusive),maxGQ=4(exclusive) ##GVCFBlock30-31=minGQ=30(inclusive),maxGQ=31(exclusive) ##GVCFBlock31-32=minGQ=31(inclusive),maxGQ=32(exclusive) ##GVCFBlock32-33=minGQ=32(inclusive),maxGQ=33(exclusive) ##GVCFBlock33-34=minGQ=33(inclusive),maxGQ=34(exclusive) ##GVCFBlock34-35=minGQ=34(inclusive),maxGQ=35(exclusive) ##GVCFBlock35-36=minGQ=35(inclusive),maxGQ=36(exclusive) ##GVCFBlock36-37=minGQ=36(inclusive),maxGQ=37(exclusive) ##GVCFBlock37-38=minGQ=37(inclusive),maxGQ=38(exclusive) ##GVCFBlock38-39=minGQ=38(inclusive),maxGQ=39(exclusive) ##GVCFBlock39-40=minGQ=39(inclusive),maxGQ=40(exclusive) ##GVCFBlock4-5=minGQ=4(inclusive),maxGQ=5(exclusive) ##GVCFBlock40-41=minGQ=40(inclusive),maxGQ=41(exclusive) ##GVCFBlock41-42=minGQ=41(inclusive),maxGQ=42(exclusive) ##GVCFBlock42-43=minGQ=42(inclusive),maxGQ=43(exclusive) ##GVCFBlock43-44=minGQ=43(inclusive),maxGQ=44(exclusive) ##GVCFBlock44-45=minGQ=44(inclusive),maxGQ=45(exclusive) ##GVCFBlock45-46=minGQ=45(inclusive),maxGQ=46(exclusive) ##GVCFBlock46-47=minGQ=46(inclusive),maxGQ=47(exclusive) ##GVCFBlock47-48=minGQ=47(inclusive),maxGQ=48(exclusive) ##GVCFBlock48-49=minGQ=48(inclusive),maxGQ=49(exclusive) ##GVCFBlock49-50=minGQ=49(inclusive),maxGQ=50(exclusive) ##GVCFBlock5-6=minGQ=5(inclusive),maxGQ=6(exclusive) ##GVCFBlock50-51=minGQ=50(inclusive),maxGQ=51(exclusive) ##GVCFBlock51-52=minGQ=51(inclusive),maxGQ=52(exclusive) ##GVCFBlock52-53=minGQ=52(inclusive),maxGQ=53(exclusive) ##GVCFBlock53-54=minGQ=53(inclusive),maxGQ=54(exclusive) ##GVCFBlock54-55=minGQ=54(inclusive),maxGQ=55(exclusive) ##GVCFBlock55-56=minGQ=55(inclusive),maxGQ=56(exclusive) ##GVCFBlock56-57=minGQ=56(inclusive),maxGQ=57(exclusive) ##GVCFBlock57-58=minGQ=57(inclusive),maxGQ=58(exclusive) ##GVCFBlock58-59=minGQ=58(inclusive),maxGQ=59(exclusive) ##GVCFBlock59-60=minGQ=59(inclusive),maxGQ=60(exclusive) ##GVCFBlock6-7=minGQ=6(inclusive),maxGQ=7(exclusive) ##GVCFBlock60-70=minGQ=60(inclusive),maxGQ=70(exclusive) ##GVCFBlock7-8=minGQ=7(inclusive),maxGQ=8(exclusive) ##GVCFBlock70-80=minGQ=70(inclusive),maxGQ=80(exclusive) ##GVCFBlock8-9=minGQ=8(inclusive),maxGQ=9(exclusive) ##GVCFBlock80-90=minGQ=80(inclusive),maxGQ=90(exclusive) ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) ##GVCFBlock99-2147483647=minGQ=99(inclusive),maxGQ=2147483647(exclusive) ##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=ClippingRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> ##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=END,Number=1,Type=Integer,Description="Stop position of the interval"> ##INFO=<ID=ExcessHet,Number=1,Type=Float,Description="Phred-scaled p-value for exact test of excess heterozygosity"> ##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=A,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=A,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=MQ,Number=1,Type=Float,Description="RMS Mapping Quality"> ##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities"> ##INFO=<ID=NEGATIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the negative training set of bad variants"> ##INFO=<ID=POSITIVE_TRAIN_SITE,Number=0,Type=Flag,Description="This variant was used to build the positive training set of good variants"> ##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth"> ##INFO=<ID=RAW_MQ,Number=1,Type=Float,Description="Raw data for RMS Mapping Quality"> ##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias"> ##INFO=<ID=SOR,Number=1,Type=Float,Description="Symmetric Odds Ratio of 2x2 contingency table to detect strand bias"> ##INFO=<ID=VQSLOD,Number=1,Type=Float,Description="Log odds 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"> ##contig=<ID=chr1,length=249250621> ##contig=<ID=chr2,length=243199373> ##contig=<ID=chr3,length=198022430> ##contig=<ID=chr4,length=191154276> ##contig=<ID=chr5,length=180915260> ##contig=<ID=chr6,length=171115067> ##contig=<ID=chr7,length=159138663> ##contig=<ID=chr8,length=146364022> ##contig=<ID=chr9,length=141213431> ##contig=<ID=chr10,length=135534747> ##contig=<ID=chr11,length=135006516> ##contig=<ID=chr12,length=133851895> ##contig=<ID=chr13,length=115169878> ##contig=<ID=chr14,length=107349540> ##contig=<ID=chr15,length=102531392> ##contig=<ID=chr16,length=90354753> ##contig=<ID=chr17,length=81195210> ##contig=<ID=chr18,length=78077248> ##contig=<ID=chr19,length=59128983> ##contig=<ID=chr20,length=63025520> ##contig=<ID=chr21,length=48129895> ##contig=<ID=chr22,length=51304566> ##contig=<ID=chrX,length=155270560> ##contig=<ID=chrY,length=59373566> ##contig=<ID=chrMT,length=16569> ##contig=<ID=chrGL000207.1,length=4262> ##contig=<ID=chrGL000226.1,length=15008> ##contig=<ID=chrGL000229.1,length=19913> ##contig=<ID=chrGL000231.1,length=27386> ##contig=<ID=chrGL000210.1,length=27682> ##contig=<ID=chrGL000239.1,length=33824> ##contig=<ID=chrGL000235.1,length=34474> ##contig=<ID=chrGL000201.1,length=36148> ##contig=<ID=chrGL000247.1,length=36422> ##contig=<ID=chrGL000245.1,length=36651> ##contig=<ID=chrGL000197.1,length=37175> ##contig=<ID=chrGL000203.1,length=37498> ##contig=<ID=chrGL000246.1,length=38154> ##contig=<ID=chrGL000249.1,length=38502> ##contig=<ID=chrGL000196.1,length=38914> ##contig=<ID=chrGL000248.1,length=39786> ##contig=<ID=chrGL000244.1,length=39929> ##contig=<ID=chrGL000238.1,length=39939> ##contig=<ID=chrGL000202.1,length=40103> ##contig=<ID=chrGL000234.1,length=40531> ##contig=<ID=chrGL000232.1,length=40652> ##contig=<ID=chrGL000206.1,length=41001> ##contig=<ID=chrGL000240.1,length=41933> ##contig=<ID=chrGL000236.1,length=41934> ##contig=<ID=chrGL000241.1,length=42152> ##contig=<ID=chrGL000243.1,length=43341> ##contig=<ID=chrGL000242.1,length=43523> ##contig=<ID=chrGL000230.1,length=43691> ##contig=<ID=chrGL000237.1,length=45867> ##contig=<ID=chrGL000233.1,length=45941> ##contig=<ID=chrGL000204.1,length=81310> ##contig=<ID=chrGL000198.1,length=90085> ##contig=<ID=chrGL000208.1,length=92689> ##contig=<ID=chrGL000191.1,length=106433> ##contig=<ID=chrGL000227.1,length=128374> ##contig=<ID=chrGL000228.1,length=129120> ##contig=<ID=chrGL000214.1,length=137718> ##contig=<ID=chrGL000221.1,length=155397> ##contig=<ID=chrGL000209.1,length=159169> ##contig=<ID=chrGL000218.1,length=161147> ##contig=<ID=chrGL000220.1,length=161802> ##contig=<ID=chrGL000213.1,length=164239> ##contig=<ID=chrGL000211.1,length=166566> ##contig=<ID=chrGL000199.1,length=169874> ##contig=<ID=chrGL000217.1,length=172149> ##contig=<ID=chrGL000216.1,length=172294> ##contig=<ID=chrGL000215.1,length=172545> ##contig=<ID=chrGL000205.1,length=174588> ##contig=<ID=chrGL000219.1,length=179198> ##contig=<ID=chrGL000224.1,length=179693> ##contig=<ID=chrGL000223.1,length=180455> ##contig=<ID=chrGL000195.1,length=182896> ##contig=<ID=chrGL000212.1,length=186858> ##contig=<ID=chrGL000222.1,length=186861> ##contig=<ID=chrGL000200.1,length=187035> ##contig=<ID=chrGL000193.1,length=189789> ##contig=<ID=chrGL000194.1,length=191469> ##contig=<ID=chrGL000225.1,length=211173> ##contig=<ID=chrGL000192.1,length=547496> ##contig=<ID=chrNC_007605,length=171823> ##reference=file:///home/wuk/Working/gnme_refrnces/Homo_sapiens_assembly19.fasta ##source=SelectVariants ##SnpEffVersion="4.3m (build 2017-05-05 18:41), by Pablo Cingolani" ##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_Rank | Genotype [ | 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'"> ##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> ##INFO=<ID=Func.refGene,Number=.,Type=String,Description="Func.refGene annotation provided by ANNOVAR"> ##INFO=<ID=Gene.refGene,Number=.,Type=String,Description="Gene.refGene annotation provided by ANNOVAR"> ##INFO=<ID=GeneDetail.refGene,Number=.,Type=String,Description="GeneDetail.refGene annotation provided by ANNOVAR"> ##INFO=<ID=ExonicFunc.refGene,Number=.,Type=String,Description="ExonicFunc.refGene annotation provided by ANNOVAR"> ##INFO=<ID=AAChange.refGene,Number=.,Type=String,Description="AAChange.refGene annotation provided by ANNOVAR"> ##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> ##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> ##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> ##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> ##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> ##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> ##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> ##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> ##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> ##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> ##INFO=<ID=RadialSVM_score,Number=.,Type=String,Description="RadialSVM_score annotation provided by ANNOVAR"> ##INFO=<ID=RadialSVM_pred,Number=.,Type=String,Description="RadialSVM_pred annotation provided by ANNOVAR"> ##INFO=<ID=LR_score,Number=.,Type=String,Description="LR_score annotation provided by ANNOVAR"> ##INFO=<ID=LR_pred,Number=.,Type=String,Description="LR_pred annotation provided by ANNOVAR"> ##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> ##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> ##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> ##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> ##INFO=<ID=phyloP46way_placental,Number=.,Type=String,Description="phyloP46way_placental annotation provided by ANNOVAR"> ##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> ##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> ##INFO=<ID=SIFT_score,Number=.,Type=String,Description="SIFT_score annotation provided by ANNOVAR"> ##INFO=<ID=SIFT_converted_rankscore,Number=.,Type=String,Description="SIFT_converted_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=SIFT_pred,Number=.,Type=String,Description="SIFT_pred annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HDIV_score,Number=.,Type=String,Description="Polyphen2_HDIV_score annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HDIV_rankscore,Number=.,Type=String,Description="Polyphen2_HDIV_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HDIV_pred,Number=.,Type=String,Description="Polyphen2_HDIV_pred annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HVAR_score,Number=.,Type=String,Description="Polyphen2_HVAR_score annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HVAR_rankscore,Number=.,Type=String,Description="Polyphen2_HVAR_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=Polyphen2_HVAR_pred,Number=.,Type=String,Description="Polyphen2_HVAR_pred annotation provided by ANNOVAR"> ##INFO=<ID=LRT_score,Number=.,Type=String,Description="LRT_score annotation provided by ANNOVAR"> ##INFO=<ID=LRT_converted_rankscore,Number=.,Type=String,Description="LRT_converted_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=LRT_pred,Number=.,Type=String,Description="LRT_pred annotation provided by ANNOVAR"> ##INFO=<ID=MutationTaster_score,Number=.,Type=String,Description="MutationTaster_score annotation provided by ANNOVAR"> ##INFO=<ID=MutationTaster_converted_rankscore,Number=.,Type=String,Description="MutationTaster_converted_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=MutationTaster_pred,Number=.,Type=String,Description="MutationTaster_pred annotation provided by ANNOVAR"> ##INFO=<ID=MutationAssessor_score,Number=.,Type=String,Description="MutationAssessor_score annotation provided by ANNOVAR"> ##INFO=<ID=MutationAssessor_score_rankscore,Number=.,Type=String,Description="MutationAssessor_score_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=MutationAssessor_pred,Number=.,Type=String,Description="MutationAssessor_pred annotation provided by ANNOVAR"> ##INFO=<ID=FATHMM_score,Number=.,Type=String,Description="FATHMM_score annotation provided by ANNOVAR"> ##INFO=<ID=FATHMM_converted_rankscore,Number=.,Type=String,Description="FATHMM_converted_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=FATHMM_pred,Number=.,Type=String,Description="FATHMM_pred annotation provided by ANNOVAR"> ##INFO=<ID=PROVEAN_score,Number=.,Type=String,Description="PROVEAN_score annotation provided by ANNOVAR"> ##INFO=<ID=PROVEAN_converted_rankscore,Number=.,Type=String,Description="PROVEAN_converted_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=PROVEAN_pred,Number=.,Type=String,Description="PROVEAN_pred annotation provided by ANNOVAR"> ##INFO=<ID=VEST3_score,Number=.,Type=String,Description="VEST3_score annotation provided by ANNOVAR"> ##INFO=<ID=VEST3_rankscore,Number=.,Type=String,Description="VEST3_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=MetaSVM_score,Number=.,Type=String,Description="MetaSVM_score annotation provided by ANNOVAR"> ##INFO=<ID=MetaSVM_rankscore,Number=.,Type=String,Description="MetaSVM_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=MetaSVM_pred,Number=.,Type=String,Description="MetaSVM_pred annotation provided by ANNOVAR"> ##INFO=<ID=MetaLR_score,Number=.,Type=String,Description="MetaLR_score annotation provided by ANNOVAR"> ##INFO=<ID=MetaLR_rankscore,Number=.,Type=String,Description="MetaLR_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=MetaLR_pred,Number=.,Type=String,Description="MetaLR_pred annotation provided by ANNOVAR"> ##INFO=<ID=M-CAP_score,Number=.,Type=String,Description="M-CAP_score annotation provided by ANNOVAR"> ##INFO=<ID=M-CAP_rankscore,Number=.,Type=String,Description="M-CAP_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=M-CAP_pred,Number=.,Type=String,Description="M-CAP_pred annotation provided by ANNOVAR"> ##INFO=<ID=CADD_raw,Number=.,Type=String,Description="CADD_raw annotation provided by ANNOVAR"> ##INFO=<ID=CADD_raw_rankscore,Number=.,Type=String,Description="CADD_raw_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=CADD_phred,Number=.,Type=String,Description="CADD_phred annotation provided by ANNOVAR"> ##INFO=<ID=DANN_score,Number=.,Type=String,Description="DANN_score annotation provided by ANNOVAR"> ##INFO=<ID=DANN_rankscore,Number=.,Type=String,Description="DANN_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=fathmm-MKL_coding_score,Number=.,Type=String,Description="fathmm-MKL_coding_score annotation provided by ANNOVAR"> ##INFO=<ID=fathmm-MKL_coding_rankscore,Number=.,Type=String,Description="fathmm-MKL_coding_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=fathmm-MKL_coding_pred,Number=.,Type=String,Description="fathmm-MKL_coding_pred annotation provided by ANNOVAR"> ##INFO=<ID=Eigen_coding_or_noncoding,Number=.,Type=String,Description="Eigen_coding_or_noncoding annotation provided by ANNOVAR"> ##INFO=<ID=Eigen-raw,Number=.,Type=String,Description="Eigen-raw annotation provided by ANNOVAR"> ##INFO=<ID=Eigen-PC-raw,Number=.,Type=String,Description="Eigen-PC-raw annotation provided by ANNOVAR"> ##INFO=<ID=GenoCanyon_score,Number=.,Type=String,Description="GenoCanyon_score annotation provided by ANNOVAR"> ##INFO=<ID=GenoCanyon_score_rankscore,Number=.,Type=String,Description="GenoCanyon_score_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=integrated_fitCons_score,Number=.,Type=String,Description="integrated_fitCons_score annotation provided by ANNOVAR"> ##INFO=<ID=integrated_fitCons_score_rankscore,Number=.,Type=String,Description="integrated_fitCons_score_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=integrated_confidence_value,Number=.,Type=String,Description="integrated_confidence_value annotation provided by ANNOVAR"> ##INFO=<ID=GERP++_RS,Number=.,Type=String,Description="GERP++_RS annotation provided by ANNOVAR"> ##INFO=<ID=GERP++_RS_rankscore,Number=.,Type=String,Description="GERP++_RS_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=phyloP100way_vertebrate,Number=.,Type=String,Description="phyloP100way_vertebrate annotation provided by ANNOVAR"> ##INFO=<ID=phyloP100way_vertebrate_rankscore,Number=.,Type=String,Description="phyloP100way_vertebrate_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=phyloP20way_mammalian,Number=.,Type=String,Description="phyloP20way_mammalian annotation provided by ANNOVAR"> ##INFO=<ID=phyloP20way_mammalian_rankscore,Number=.,Type=String,Description="phyloP20way_mammalian_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=phastCons100way_vertebrate,Number=.,Type=String,Description="phastCons100way_vertebrate annotation provided by ANNOVAR"> ##INFO=<ID=phastCons100way_vertebrate_rankscore,Number=.,Type=String,Description="phastCons100way_vertebrate_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=phastCons20way_mammalian,Number=.,Type=String,Description="phastCons20way_mammalian annotation provided by ANNOVAR"> ##INFO=<ID=phastCons20way_mammalian_rankscore,Number=.,Type=String,Description="phastCons20way_mammalian_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=SiPhy_29way_logOdds,Number=.,Type=String,Description="SiPhy_29way_logOdds annotation provided by ANNOVAR"> ##INFO=<ID=SiPhy_29way_logOdds_rankscore,Number=.,Type=String,Description="SiPhy_29way_logOdds_rankscore annotation provided by ANNOVAR"> ##INFO=<ID=Interpro_domain,Number=.,Type=String,Description="Interpro_domain annotation provided by ANNOVAR"> ##INFO=<ID=GTEx_V6_gene,Number=.,Type=String,Description="GTEx_V6_gene annotation provided by ANNOVAR"> ##INFO=<ID=GTEx_V6_tissue,Number=.,Type=String,Description="GTEx_V6_tissue annotation provided by ANNOVAR"> ##INFO=<ID=dbscSNV_ADA_SCORE,Number=.,Type=String,Description="dbscSNV_ADA_SCORE annotation provided by ANNOVAR"> ##INFO=<ID=dbscSNV_RF_SCORE,Number=.,Type=String,Description="dbscSNV_RF_SCORE annotation provided by ANNOVAR"> ##INFO=<ID=InterVar(automated),Number=.,Type=String,Description="InterVar(automated) annotation provided by ANNOVAR"> ##INFO=<ID=PVS1,Number=.,Type=String,Description="PVS1 annotation provided by ANNOVAR"> ##INFO=<ID=PS1,Number=.,Type=String,Description="PS1 annotation provided by ANNOVAR"> ##INFO=<ID=PS2,Number=.,Type=String,Description="PS2 annotation provided by ANNOVAR"> ##INFO=<ID=PS3,Number=.,Type=String,Description="PS3 annotation provided by ANNOVAR"> ##INFO=<ID=PS4,Number=.,Type=String,Description="PS4 annotation provided by ANNOVAR"> ##INFO=<ID=PM1,Number=.,Type=String,Description="PM1 annotation provided by ANNOVAR"> ##INFO=<ID=PM2,Number=.,Type=String,Description="PM2 annotation provided by ANNOVAR"> ##INFO=<ID=PM3,Number=.,Type=String,Description="PM3 annotation provided by ANNOVAR"> ##INFO=<ID=PM4,Number=.,Type=String,Description="PM4 annotation provided by ANNOVAR"> ##INFO=<ID=PM5,Number=.,Type=String,Description="PM5 annotation provided by ANNOVAR"> ##INFO=<ID=PM6,Number=.,Type=String,Description="PM6 annotation provided by ANNOVAR"> ##INFO=<ID=PP1,Number=.,Type=String,Description="PP1 annotation provided by ANNOVAR"> ##INFO=<ID=PP2,Number=.,Type=String,Description="PP2 annotation provided by ANNOVAR"> ##INFO=<ID=PP3,Number=.,Type=String,Description="PP3 annotation provided by ANNOVAR"> ##INFO=<ID=PP4,Number=.,Type=String,Description="PP4 annotation provided by ANNOVAR"> ##INFO=<ID=PP5,Number=.,Type=String,Description="PP5 annotation provided by ANNOVAR"> ##INFO=<ID=BA1,Number=.,Type=String,Description="BA1 annotation provided by ANNOVAR"> ##INFO=<ID=BS1,Number=.,Type=String,Description="BS1 annotation provided by ANNOVAR"> ##INFO=<ID=BS2,Number=.,Type=String,Description="BS2 annotation provided by ANNOVAR"> ##INFO=<ID=BS3,Number=.,Type=String,Description="BS3 annotation provided by ANNOVAR"> ##INFO=<ID=BS4,Number=.,Type=String,Description="BS4 annotation provided by ANNOVAR"> ##INFO=<ID=BP1,Number=.,Type=String,Description="BP1 annotation provided by ANNOVAR"> ##INFO=<ID=BP2,Number=.,Type=String,Description="BP2 annotation provided by ANNOVAR"> ##INFO=<ID=BP3,Number=.,Type=String,Description="BP3 annotation provided by ANNOVAR"> ##INFO=<ID=BP4,Number=.,Type=String,Description="BP4 annotation provided by ANNOVAR"> ##INFO=<ID=BP5,Number=.,Type=String,Description="BP5 annotation provided by ANNOVAR"> ##INFO=<ID=BP6,Number=.,Type=String,Description="BP6 annotation provided by ANNOVAR"> ##INFO=<ID=BP7,Number=.,Type=String,Description="BP7 annotation provided by ANNOVAR"> ##INFO=<ID=esp6500siv2_ea,Number=1,Type=Float,Description="esp6500siv2_ea annotation provided by ANNOVAR"> ##INFO=<ID=esp6500siv2_all,Number=1,Type=Float,Description="esp6500siv2_all annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_ALL,Number=.,Type=String,Description="ExAC_ALL annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_AFR,Number=.,Type=String,Description="ExAC_AFR annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_AMR,Number=.,Type=String,Description="ExAC_AMR annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_EAS,Number=.,Type=String,Description="ExAC_EAS annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_FIN,Number=.,Type=String,Description="ExAC_FIN annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_NFE,Number=.,Type=String,Description="ExAC_NFE annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_OTH,Number=.,Type=String,Description="ExAC_OTH annotation provided by ANNOVAR"> ##INFO=<ID=ExAC_SAS,Number=.,Type=String,Description="ExAC_SAS annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_ALL,Number=.,Type=String,Description="gnomAD_exome_ALL annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_AFR,Number=.,Type=String,Description="gnomAD_exome_AFR annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_AMR,Number=.,Type=String,Description="gnomAD_exome_AMR annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_ASJ,Number=.,Type=String,Description="gnomAD_exome_ASJ annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_EAS,Number=.,Type=String,Description="gnomAD_exome_EAS annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_FIN,Number=.,Type=String,Description="gnomAD_exome_FIN annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_NFE,Number=.,Type=String,Description="gnomAD_exome_NFE annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_OTH,Number=.,Type=String,Description="gnomAD_exome_OTH annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_exome_SAS,Number=.,Type=String,Description="gnomAD_exome_SAS annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_ALL,Number=.,Type=String,Description="gnomAD_genome_ALL annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_AFR,Number=.,Type=String,Description="gnomAD_genome_AFR annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_AMR,Number=.,Type=String,Description="gnomAD_genome_AMR annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_ASJ,Number=.,Type=String,Description="gnomAD_genome_ASJ annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_EAS,Number=.,Type=String,Description="gnomAD_genome_EAS annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_FIN,Number=.,Type=String,Description="gnomAD_genome_FIN annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_NFE,Number=.,Type=String,Description="gnomAD_genome_NFE annotation provided by ANNOVAR"> ##INFO=<ID=gnomAD_genome_OTH,Number=.,Type=String,Description="gnomAD_genome_OTH annotation provided by ANNOVAR"> ##INFO=<ID=1000g2015aug_all,Number=1,Type=Float,Description="1000g2015aug_all annotation provided by ANNOVAR"> ##INFO=<ID=MCAP,Number=.,Type=String,Description="MCAP annotation provided by ANNOVAR"> ##INFO=<ID=REVEL,Number=.,Type=String,Description="REVEL annotation provided by ANNOVAR"> ##INFO=<ID=GWAVA_region_score,Number=.,Type=String,Description="GWAVA_region_score annotation provided by ANNOVAR"> ##INFO=<ID=GWAVA_tss_score,Number=.,Type=String,Description="GWAVA_tss_score annotation provided by ANNOVAR"> ##INFO=<ID=GWAVA_unmatched_score,Number=.,Type=String,Description="GWAVA_unmatched_score annotation provided by ANNOVAR"> ##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> ##INFO=<ID=ANNOVAR_DATE,Number=1,Type=String,Description="Flag the start of ANNOVAR annotation for one alternative allele"> ##INFO=<ID=CADD13_RawScore,Number=.,Type=String,Description="CADD13_RawScore annotation provided by ANNOVAR"> ##INFO=<ID=CADD13_PHRED,Number=.,Type=String,Description="CADD13_PHRED annotation provided by ANNOVAR"> ##INFO=<ID=ALLELE_END,Number=0,Type=Flag,Description="Flag the end of ANNOVAR annotation for one alternative allele"> ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> ##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same"> ##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)"> ##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)"> ##INFO=<ID=IS,Number=2,Type=Float,Description="Maximum number of reads supporting an indel and fraction of indel reads"> ##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies"> ##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3"> ##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint"> ##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio"> ##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio"> ##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias"> ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> ##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2."> ##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples."> ##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2."> ##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2."> ##INFO=<ID=QBD,Number=1,Type=Float,Description="Quality by Depth: QUAL/#reads"> ##INFO=<ID=RPB,Number=1,Type=Float,Description="Read Position Bias"> ##INFO=<ID=MDV,Number=1,Type=Integer,Description="Maximum number of high-quality nonRef reads in samples"> ##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias (v2) for filtering splice-site artefacts in RNA-seq data. Note: this version may be broken."> ##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)"> ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality non-reference bases"> ##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value"> #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample01 sample02 sample03 chr22 17565035 rs4819554 G A 3.39e+03 PASS AC=6;AF=1.00;AN=6;DB;DP=96;ExcessHet=3.0103;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=60.00;POSITIVE_TRAIN_SITE;QD=27.46;SOR=1.167;VQSLOD=6.60;culprit=QD;EFF=UPSTREAM(MODIFIER||814||866|IL17RA|protein_coding|CODING|ENST00000319363||A),UPSTREAM(MODIFIER||809|||IL17RA|processed_transcript|CODING|ENST00000477874||A),UPSTREAM(MODIFIER||912|||IL17RA|retained_intron|CODING|ENST00000459971||A),DOWNSTREAM(MODIFIER||2689|||AC006946.17|lincRNA|NON_CODING|ENST00000609791||A),INTERGENIC(MODIFIER||||||||||A);ANNOVAR_DATE=2016-02-01;Func.refGene=upstream;Gene.refGene=IL17RA;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;gnomAD_exome_ALL=.;gnomAD_exome_AFR=.;gnomAD_exome_AMR=.;gnomAD_exome_ASJ=.;gnomAD_exome_EAS=.;gnomAD_exome_FIN=.;gnomAD_exome_NFE=.;gnomAD_exome_OTH=.;gnomAD_exome_SAS=.;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.766973;MCAP=.;REVEL=.;GWAVA_region_score=0.35;GWAVA_tss_score=0.57;GWAVA_unmatched_score=182;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=0.154414;CADD13_PHRED=4.193;ALLELE_END GT:AD:DP:GQ:PL 1/1:.:40:99:255,120,0 1/1:.:25:75:255,75,0 1/1:.:30:89:255,89,0 chr22 21349676 rs412470 T A 423 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-8.270e-01;ClippingRankSum=0.00;DB;DP=92;ExcessHet=3.0103;FS=1.623;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;QD=16.93;ReadPosRankSum=0.120;SOR=0.368;VQSLOD=7.61;culprit=MQRankSum;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tct/Act|S92T|97|LZTR1|nonsense_mediated_decay|CODING|ENST00000415354|4|A),SPLICE_SITE_REGION+EXON(LOW|||||LZTR1|retained_intron|CODING|ENST00000464807|2|A),SYNONYMOUS_CODING(LOW|SILENT|gcT/gcA|A81|110|LZTR1|nonsense_mediated_decay|CODING|ENST00000439171|3|A|WARNING_TRANSCRIPT_NO_START_CODON),UPSTREAM(MODIFIER||401|||LZTR1|retained_intron|CODING|ENST00000498649||A),UPSTREAM(MODIFIER||609||157|LZTR1|protein_coding|CODING|ENST00000415817||A|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||4385||309|THAP7|protein_coding|CODING|ENST00000215742||A),DOWNSTREAM(MODIFIER||3702||117|LZTR1|nonsense_mediated_decay|CODING|ENST00000414985||A),DOWNSTREAM(MODIFIER||3708|||LZTR1|processed_transcript|CODING|ENST00000480895||A),DOWNSTREAM(MODIFIER||2539|||LZTR1|processed_transcript|CODING|ENST00000497716||A),DOWNSTREAM(MODIFIER||2855|||LZTR1|retained_intron|CODING|ENST00000461510||A),DOWNSTREAM(MODIFIER||1087|||LZTR1|retained_intron|CODING|ENST00000492480||A),DOWNSTREAM(MODIFIER||3717|||THAP7|retained_intron|CODING|ENST00000498406||A),DOWNSTREAM(MODIFIER||4386|||THAP7|retained_intron|CODING|ENST00000471073||A),DOWNSTREAM(MODIFIER||4390||309|THAP7|protein_coding|CODING|ENST00000399133||A),DOWNSTREAM(MODIFIER||4415|||THAP7|retained_intron|CODING|ENST00000476667||A),DOWNSTREAM(MODIFIER||4843|||THAP7|retained_intron|CODING|ENST00000466670||A),DOWNSTREAM(MODIFIER||4885|||THAP7|retained_intron|CODING|ENST00000488975||A),INTRON(MODIFIER||||840|LZTR1|protein_coding|CODING|ENST00000215739|16|A),INTRON(MODIFIER|||||LZTR1|processed_transcript|CODING|ENST00000479606|17|A),INTRON(MODIFIER||||821|LZTR1|protein_coding|CODING|ENST00000389355|15|A),INTRON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000495142|2|A),INTRON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000491432|2|A),INTRON(MODIFIER||||54|LZTR1|nonsense_mediated_decay|CODING|ENST00000452988|1|A|WARNING_TRANSCRIPT_NO_START_CODON),EXON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000463909|1|A);ANNOVAR_DATE=2016-02-01;Func.refGene=intronic;Gene.refGene=LZTR1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=0.1346;ExAC_AFR=0.0420;ExAC_AMR=0.1088;ExAC_EAS=0.1829;ExAC_FIN=0.1389;ExAC_NFE=0.1446;ExAC_OTH=0.1234;ExAC_SAS=0.1368;gnomAD_exome_ALL=0.1296;gnomAD_exome_AFR=0.0351;gnomAD_exome_AMR=0.0855;gnomAD_exome_ASJ=0.1562;gnomAD_exome_EAS=0.1602;gnomAD_exome_FIN=0.1292;gnomAD_exome_NFE=0.1493;gnomAD_exome_OTH=0.1390;gnomAD_exome_SAS=0.1339;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.105232;MCAP=.;REVEL=.;GWAVA_region_score=0.21;GWAVA_tss_score=0.06;GWAVA_unmatched_score=182;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=0.350070;CADD13_PHRED=6.167;ALLELE_END GT:AD:DP:GQ:PGT:PID:PL 0/0:.:32:90:.:.:0,90,255 0/1:.:25:99:.:.:255,0,255 0/0:.:35:93:.:.:0,93,255 chr22 21349677 rs376419 C T 423 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=-1.349e+00;ClippingRankSum=0.00;DB;DP=92;ExcessHet=3.0103;FS=1.623;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=16.93;ReadPosRankSum=0.235;SOR=0.368;VQSLOD=8.80;culprit=MQRankSum;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tCt/tTt|S92F|97|LZTR1|nonsense_mediated_decay|CODING|ENST00000415354|4|T),NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Ctc/Ttc|L82F|110|LZTR1|nonsense_mediated_decay|CODING|ENST00000439171|3|T|WARNING_TRANSCRIPT_NO_START_CODON),SPLICE_SITE_REGION+EXON(LOW|||||LZTR1|retained_intron|CODING|ENST00000464807|2|T),UPSTREAM(MODIFIER||400|||LZTR1|retained_intron|CODING|ENST00000498649||T),UPSTREAM(MODIFIER||608||157|LZTR1|protein_coding|CODING|ENST00000415817||T|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||4384||309|THAP7|protein_coding|CODING|ENST00000215742||T),DOWNSTREAM(MODIFIER||3703||117|LZTR1|nonsense_mediated_decay|CODING|ENST00000414985||T),DOWNSTREAM(MODIFIER||3709|||LZTR1|processed_transcript|CODING|ENST00000480895||T),DOWNSTREAM(MODIFIER||2540|||LZTR1|processed_transcript|CODING|ENST00000497716||T),DOWNSTREAM(MODIFIER||2856|||LZTR1|retained_intron|CODING|ENST00000461510||T),DOWNSTREAM(MODIFIER||1088|||LZTR1|retained_intron|CODING|ENST00000492480||T),DOWNSTREAM(MODIFIER||3716|||THAP7|retained_intron|CODING|ENST00000498406||T),DOWNSTREAM(MODIFIER||4385|||THAP7|retained_intron|CODING|ENST00000471073||T),DOWNSTREAM(MODIFIER||4389||309|THAP7|protein_coding|CODING|ENST00000399133||T),DOWNSTREAM(MODIFIER||4414|||THAP7|retained_intron|CODING|ENST00000476667||T),DOWNSTREAM(MODIFIER||4842|||THAP7|retained_intron|CODING|ENST00000466670||T),DOWNSTREAM(MODIFIER||4884|||THAP7|retained_intron|CODING|ENST00000488975||T),INTRON(MODIFIER||||840|LZTR1|protein_coding|CODING|ENST00000215739|16|T),INTRON(MODIFIER|||||LZTR1|processed_transcript|CODING|ENST00000479606|17|T),INTRON(MODIFIER||||821|LZTR1|protein_coding|CODING|ENST00000389355|15|T),INTRON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000495142|2|T),INTRON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000491432|2|T),INTRON(MODIFIER||||54|LZTR1|nonsense_mediated_decay|CODING|ENST00000452988|1|T|WARNING_TRANSCRIPT_NO_START_CODON),EXON(MODIFIER|||||LZTR1|retained_intron|CODING|ENST00000463909|1|T);ANNOVAR_DATE=2016-02-01;Func.refGene=intronic;Gene.refGene=LZTR1;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=0.1347;ExAC_AFR=0.0420;ExAC_AMR=0.1088;ExAC_EAS=0.1829;ExAC_FIN=0.1389;ExAC_NFE=0.1447;ExAC_OTH=0.1234;ExAC_SAS=0.1368;gnomAD_exome_ALL=0.1296;gnomAD_exome_AFR=0.0351;gnomAD_exome_AMR=0.0855;gnomAD_exome_ASJ=0.1563;gnomAD_exome_EAS=0.1602;gnomAD_exome_FIN=0.1292;gnomAD_exome_NFE=0.1493;gnomAD_exome_OTH=0.1391;gnomAD_exome_SAS=0.1339;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.105232;MCAP=.;REVEL=.;GWAVA_region_score=0.19;GWAVA_tss_score=0.08;GWAVA_unmatched_score=182;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=0.349663;CADD13_PHRED=6.163;ALLELE_END GT:AD:DP:GQ:PGT:PID:PL 0/0:.:32:90:.:.:0,90,255 0/1:.:25:99:.:.:255,0,255 0/0:.:35:93:.:.:0,93,255 chr22 22262093 rs76843711 C A 1.17e+03 PASS AC=2;AF=0.333;AN=6;BaseQRankSum=3.06;ClippingRankSum=0.00;DB;DP=117;ExcessHet=3.9794;FS=2.960;MLEAC=2;MLEAF=0.333;MQ=60.00;MQRankSum=0.00;POSITIVE_TRAIN_SITE;QD=14.26;ReadPosRankSum=-1.830e-01;SOR=1.127;VQSLOD=9.04;culprit=MQRankSum;EFF=INTERGENIC(MODIFIER||||||||||A);ANNOVAR_DATE=2016-02-01;Func.refGene=intergenic;Gene.refGene=MAPK1,PPM1F;GeneDetail.refGene=dist\x3d40123\x3bdist\x3d11699;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=.;ExAC_AFR=.;ExAC_AMR=.;ExAC_EAS=.;ExAC_FIN=.;ExAC_NFE=.;ExAC_OTH=.;ExAC_SAS=.;gnomAD_exome_ALL=.;gnomAD_exome_AFR=.;gnomAD_exome_AMR=.;gnomAD_exome_ASJ=.;gnomAD_exome_EAS=.;gnomAD_exome_FIN=.;gnomAD_exome_NFE=.;gnomAD_exome_OTH=.;gnomAD_exome_SAS=.;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.0696885;MCAP=.;REVEL=.;GWAVA_region_score=0.3;GWAVA_tss_score=0.12;GWAVA_unmatched_score=182;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=0.097641;CADD13_PHRED=3.583;ALLELE_END GT:AD:DP:GQ:PL 0/0:.:34:99:0,99,255 0/1:.:42:99:255,0,255 0/1:.:40:99:255,0,255 chr22 23247169 rs527511481 T G 719 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=2.62;ClippingRankSum=0.00;DB;DP=121;ExcessHet=3.6798;FS=10.117;MLEAC=1;MLEAF=0.167;MQ=49.77;MQRankSum=-4.022e+00;NEGATIVE_TRAIN_SITE;QD=25.67;ReadPosRankSum=-9.600e-02;SOR=2.252;VQSLOD=-2.025e+00;culprit=SOR;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|Tgg/Ggg|W39G|49|IGLJ3|IG_J_gene|CODING|ENST00000390324|1|G|WARNING_TRANSCRIPT_INCOMPLETE),UPSTREAM(MODIFIER||1343||105|IGLC3|IG_C_gene|CODING|ENST00000390325||G|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||3552||105|IGLC2|IG_C_gene|CODING|ENST00000390323||G|WARNING_TRANSCRIPT_NO_START_CODON);ANNOVAR_DATE=2016-02-01;Func.refGene=intergenic;Gene.refGene=IGLL5,RSPH14;GeneDetail.refGene=dist\x3d9156\x3bdist\x3d154424;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=0.1262;ExAC_AFR=0.2077;ExAC_AMR=0.0572;ExAC_EAS=0.1866;ExAC_FIN=0.17;ExAC_NFE=0.1171;ExAC_OTH=0.125;ExAC_SAS=0.1166;gnomAD_exome_ALL=0.0960;gnomAD_exome_AFR=0.2037;gnomAD_exome_AMR=0.0765;gnomAD_exome_ASJ=0.0650;gnomAD_exome_EAS=0.2503;gnomAD_exome_FIN=0.1001;gnomAD_exome_NFE=0.0779;gnomAD_exome_OTH=0.0925;gnomAD_exome_SAS=0.0712;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.105032;MCAP=.;REVEL=.;GWAVA_region_score=.;GWAVA_tss_score=.;GWAVA_unmatched_score=.;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=-2.133468;CADD13_PHRED=0.001;ALLELE_END GT:AD:DP:GQ:PGT:PID:PL 0/0:.:53:99:.:.:0,120,255 0/1:.:28:99:.:.:255,0,255 0/0:.:40:0:.:.:0,0,255 chr22 23247170 rs540954398 G T 716 PASS AC=1;AF=0.167;AN=6;BaseQRankSum=1.73;ClippingRankSum=0.00;DB;DP=122;ExcessHet=3.0103;FS=9.423;MLEAC=1;MLEAF=0.167;MQ=49.47;MQRankSum=-4.088e+00;NEGATIVE_TRAIN_SITE;QD=24.70;ReadPosRankSum=-3.910e-01;SOR=1.911;VQSLOD=-2.392e+00;culprit=SOR;EFF=NON_SYNONYMOUS_CODING(MODERATE|MISSENSE|tGg/tTg|W39L|49|IGLJ3|IG_J_gene|CODING|ENST00000390324|1|T|WARNING_TRANSCRIPT_INCOMPLETE),UPSTREAM(MODIFIER||1342||105|IGLC3|IG_C_gene|CODING|ENST00000390325||T|WARNING_TRANSCRIPT_NO_START_CODON),DOWNSTREAM(MODIFIER||3553||105|IGLC2|IG_C_gene|CODING|ENST00000390323||T|WARNING_TRANSCRIPT_NO_START_CODON);ANNOVAR_DATE=2016-02-01;Func.refGene=intergenic;Gene.refGene=IGLL5,RSPH14;GeneDetail.refGene=dist\x3d9157\x3bdist\x3d154423;ExonicFunc.refGene=.;AAChange.refGene=.;SIFT_score=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_pred=.;RadialSVM_score=.;RadialSVM_pred=.;LR_score=.;LR_pred=.;VEST3_score=.;CADD_raw=.;CADD_phred=.;GERP++_RS=.;phyloP46way_placental=.;phyloP100way_vertebrate=.;SiPhy_29way_logOdds=.;SIFT_score=.;SIFT_converted_rankscore=.;SIFT_pred=.;Polyphen2_HDIV_score=.;Polyphen2_HDIV_rankscore=.;Polyphen2_HDIV_pred=.;Polyphen2_HVAR_score=.;Polyphen2_HVAR_rankscore=.;Polyphen2_HVAR_pred=.;LRT_score=.;LRT_converted_rankscore=.;LRT_pred=.;MutationTaster_score=.;MutationTaster_converted_rankscore=.;MutationTaster_pred=.;MutationAssessor_score=.;MutationAssessor_score_rankscore=.;MutationAssessor_pred=.;FATHMM_score=.;FATHMM_converted_rankscore=.;FATHMM_pred=.;PROVEAN_score=.;PROVEAN_converted_rankscore=.;PROVEAN_pred=.;VEST3_score=.;VEST3_rankscore=.;MetaSVM_score=.;MetaSVM_rankscore=.;MetaSVM_pred=.;MetaLR_score=.;MetaLR_rankscore=.;MetaLR_pred=.;M-CAP_score=.;M-CAP_rankscore=.;M-CAP_pred=.;CADD_raw=.;CADD_raw_rankscore=.;CADD_phred=.;DANN_score=.;DANN_rankscore=.;fathmm-MKL_coding_score=.;fathmm-MKL_coding_rankscore=.;fathmm-MKL_coding_pred=.;Eigen_coding_or_noncoding=.;Eigen-raw=.;Eigen-PC-raw=.;GenoCanyon_score=.;GenoCanyon_score_rankscore=.;integrated_fitCons_score=.;integrated_fitCons_score_rankscore=.;integrated_confidence_value=.;GERP++_RS=.;GERP++_RS_rankscore=.;phyloP100way_vertebrate=.;phyloP100way_vertebrate_rankscore=.;phyloP20way_mammalian=.;phyloP20way_mammalian_rankscore=.;phastCons100way_vertebrate=.;phastCons100way_vertebrate_rankscore=.;phastCons20way_mammalian=.;phastCons20way_mammalian_rankscore=.;SiPhy_29way_logOdds=.;SiPhy_29way_logOdds_rankscore=.;Interpro_domain=.;GTEx_V6_gene=.;GTEx_V6_tissue=.;dbscSNV_ADA_SCORE=.;dbscSNV_RF_SCORE=.;InterVar(automated)=.;PVS1=.;PS1=.;PS2=.;PS3=.;PS4=.;PM1=.;PM2=.;PM3=.;PM4=.;PM5=.;PM6=.;PP1=.;PP2=.;PP3=.;PP4=.;PP5=.;BA1=.;BS1=.;BS2=.;BS3=.;BS4=.;BP1=.;BP2=.;BP3=.;BP4=.;BP5=.;BP6=.;BP7=.;esp6500siv2_ea=.;esp6500siv2_all=.;ExAC_ALL=0.1225;ExAC_AFR=0.1998;ExAC_AMR=0.0548;ExAC_EAS=0.1777;ExAC_FIN=0.1607;ExAC_NFE=0.1143;ExAC_OTH=0.1207;ExAC_SAS=0.1145;gnomAD_exome_ALL=0.0906;gnomAD_exome_AFR=0.1949;gnomAD_exome_AMR=0.0726;gnomAD_exome_ASJ=0.0615;gnomAD_exome_EAS=0.2403;gnomAD_exome_FIN=0.0928;gnomAD_exome_NFE=0.0729;gnomAD_exome_OTH=0.0885;gnomAD_exome_SAS=0.0669;gnomAD_genome_ALL=.;gnomAD_genome_AFR=.;gnomAD_genome_AMR=.;gnomAD_genome_ASJ=.;gnomAD_genome_EAS=.;gnomAD_genome_FIN=.;gnomAD_genome_NFE=.;gnomAD_genome_OTH=.;1000g2015aug_all=0.103035;MCAP=.;REVEL=.;GWAVA_region_score=.;GWAVA_tss_score=.;GWAVA_unmatched_score=.;ALLELE_END;ANNOVAR_DATE=2016-02-01;CADD13_RawScore=-1.839588;CADD13_PHRED=0.002;ALLELE_END GT:AD:DP:GQ:PGT:PID:PL 0/0:.:53:99:.:.:0,120,255 0/1:.:29:99:.:.:255,0,255 0/0:.:40:15:.:.:0,15,255