VCF Fields ---------- with Number=R (value for reference and each alternate allele) ============= gnomAD: AD Allelic depths for the ref and alt alleles in the order listed with Number=A (value for each alternate allele) ============= gnomAD: AB_HIST_ALT Histogram for Allele Balance in heterozygous individuals for each allele; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 AB_MEDIAN Median allele balance in heterozygote carriers of each allele AC Allele count in genotypes, for each ALT allele, in the same order as listed AC_AFR Allele count in African/African American genotypes, for each ALT allele, in the same order as listed AC_AFR_Female Allele count in African/African American Female genotypes, for each ALT allele, in the same order as listed AC_AFR_Male Allele count in African/African American Male genotypes, for each ALT allele, in the same order as listed AC_AMR Allele count in Admixed American genotypes, for each ALT allele, in the same order as listed AC_AMR_Female Allele count in Admixed American Female genotypes, for each ALT allele, in the same order as listed AC_AMR_Male Allele count in Admixed American Male genotypes, for each ALT allele, in the same order as listed AC_ASJ Allele count in Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed AC_ASJ_Female Allele count in Ashkenazi Jewish Female genotypes, for each ALT allele, in the same order as listed AC_ASJ_Male Allele count in Ashkenazi Jewish Male genotypes, for each ALT allele, in the same order as listed AC_EAS Allele count in East Asian genotypes, for each ALT allele, in the same order as listed AC_EAS_Female Allele count in East Asian Female genotypes, for each ALT allele, in the same order as listed AC_EAS_Male Allele count in East Asian Male genotypes, for each ALT allele, in the same order as listed AC_Female Allele count in Female genotypes, for each ALT allele, in the same order as listed AC_FIN Allele count in Finnish genotypes, for each ALT allele, in the same order as listed AC_FIN_Female Allele count in Finnish Female genotypes, for each ALT allele, in the same order as listed AC_FIN_Male Allele count in Finnish Male genotypes, for each ALT allele, in the same order as listed AC_Male Allele count in Male genotypes, for each ALT allele, in the same order as listed AC_NFE Allele count in Non-Finnish European genotypes, for each ALT allele, in the same order as listed AC_NFE_Female Allele count in Non-Finnish European Female genotypes, for each ALT allele, in the same order as listed AC_NFE_Male Allele count in Non-Finnish European Male genotypes, for each ALT allele, in the same order as listed AC_OTH Allele count in Other (population not assigned) genotypes, for each ALT allele, in the same order as listed AC_OTH_Female Allele count in Other (population not assigned) Female genotypes, for each ALT allele, in the same order as listed AC_OTH_Male Allele count in Other (population not assigned) Male genotypes, for each ALT allele, in the same order as listed AC_POPMAX AC in the population with the max AF AC_raw Allele counts before filtering low-confidence genotypes, for each ALT allele, in the same order as listed AC_SAS Allele count in South Asian genotypes, for each ALT allele, in the same order as listed AC_SAS_Female Allele count in South Asian Female genotypes, for each ALT allele, in the same order as listed AC_SAS_Male Allele count in South Asian Male genotypes, for each ALT allele, in the same order as listed AF Allele Frequency among genotypes, for each ALT allele, in the same order as listed AF_AFR Allele Frequency among African/African American genotypes, for each ALT allele, in the same order as listed AF_AFR_Female Allele Frequency among African/African American Female genotypes, for each ALT allele, in the same order as listed AF_AFR_Male Allele Frequency among African/African American Male genotypes, for each ALT allele, in the same order as listed AF_AMR Allele Frequency among Admixed American genotypes, for each ALT allele, in the same order as listed AF_AMR_Female Allele Frequency among Admixed American Female genotypes, for each ALT allele, in the same order as listed AF_AMR_Male Allele Frequency among Admixed American Male genotypes, for each ALT allele, in the same order as listed AF_ASJ Allele Frequency among Ashkenazi Jewish genotypes, for each ALT allele, in the same order as listed AF_ASJ_Female Allele Frequency among Ashkenazi Jewish Female genotypes, for each ALT allele, in the same order as listed AF_ASJ_Male Allele Frequency among Ashkenazi Jewish Male genotypes, for each ALT allele, in the same order as listed AF_EAS Allele Frequency among East Asian genotypes, for each ALT allele, in the same order as listed AF_EAS_Female Allele Frequency among East Asian Female genotypes, for each ALT allele, in the same order as listed AF_EAS_Male Allele Frequency among East Asian Male genotypes, for each ALT allele, in the same order as listed AF_Female Allele Frequency among Female genotypes, for each ALT allele, in the same order as listed AF_FIN Allele Frequency among Finnish genotypes, for each ALT allele, in the same order as listed AF_FIN_Female Allele Frequency among Finnish Female genotypes, for each ALT allele, in the same order as listed AF_FIN_Male Allele Frequency among Finnish Male genotypes, for each ALT allele, in the same order as listed AF_Male Allele Frequency among Male genotypes, for each ALT allele, in the same order as listed AF_NFE Allele Frequency among Non-Finnish European genotypes, for each ALT allele, in the same order as listed AF_NFE_Female Allele Frequency among Non-Finnish European Female genotypes, for each ALT allele, in the same order as listed AF_NFE_Male Allele Frequency among Non-Finnish European Male genotypes, for each ALT allele, in the same order as listed AF_OTH Allele Frequency among Other (population not assigned) genotypes, for each ALT allele, in the same order as listed AF_OTH_Female Allele Frequency among Other (population not assigned) Female genotypes, for each ALT allele, in the same order as listed AF_OTH_Male Allele Frequency among Other (population not assigned) Male genotypes, for each ALT allele, in the same order as listed AF_POPMAX Maximum Allele Frequency across populations (excluding OTH) AF_raw Allele frequency before filtering low-confidence genotypes, for each ALT allele, in the same order as listed AF_SAS Allele Frequency among South Asian genotypes, for each ALT allele, in the same order as listed AF_SAS_Female Allele Frequency among South Asian Female genotypes, for each ALT allele, in the same order as listed AF_SAS_Male Allele Frequency among South Asian Male genotypes, for each ALT allele, in the same order as listed AN_POPMAX AN in the population with the max AF AS_FilterStatus Random Forests filter status for each allele AS_RF Random Forests probability for each allele DP_HIST_ALT Histogram for DP for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 DP_MEDIAN Median DP in carriers of each allele DREF_MEDIAN Median dosage of homozygous reference in carriers of each allele GQ_HIST_ALT Histogram for GQ for each allele; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 GQ_MEDIAN Median GQ in carriers of each allele Hemi Count of hemizygous individuals Hemi_AFR Count of hemizygous African/African American individuals Hemi_AMR Count of hemizygous Admixed American individuals Hemi_ASJ Count of hemizygous Ashkenazi Jewish individuals Hemi_EAS Count of hemizygous East Asian individuals Hemi_FIN Count of hemizygous Finnish individuals Hemi_NFE Count of hemizygous Non-Finnish European individuals Hemi_OTH Count of hemizygous Other (population not assigned) individuals Hemi_raw Count of hemizygous individuals in raw genotypes before filtering low-confidence genotypes Hemi_SAS Count of hemizygous South Asian individuals Hom Count of homozygous individuals Hom_AFR Count of homozygous African/African American individuals Hom_AMR Count of homozygous Admixed American individuals Hom_ASJ Count of homozygous Ashkenazi Jewish individuals Hom_EAS Count of homozygous East Asian individuals Hom_Female Count of homozygous Female individuals Hom_FIN Count of homozygous Finnish individuals Hom_Male Count of homozygous Male individuals Hom_NFE Count of homozygous Non-Finnish European individuals Hom_OTH Count of homozygous Other (population not assigned) individuals Hom_raw Count of homozygous individuals in raw genotypes before filtering low-confidence genotypes Hom_SAS Count of homozygous South Asian individuals POPMAX Population with max AF aphid: MLEAC Maximum likelihood expectation (MLE) for the allele counts ... for each ALT allele, in the same order as listed MLEAF Maximum likelihood expectation (MLE) for the allele frequency ... for each ALT allele, in the same order as listed with Number=1 ============= gnomAD: AB_HIST_ALL Histogram for Allele Balance in heterozygous individuals; 100*AD[i_alt]/sum(AD); Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 AN Total number of alleles in called genotypes AN_AFR Total number of alleles in African/African American called genotypes AN_AFR_Female Total number of alleles in African/African American Female called genotypes AN_AFR_Male Total number of alleles in African/African American Male called genotypes AN_AMR Total number of alleles in Admixed American called genotypes AN_AMR_Female Total number of alleles in Admixed American Female called genotypes AN_AMR_Male Total number of alleles in Admixed American Male called genotypes AN_ASJ Total number of alleles in Ashkenazi Jewish called genotypes AN_ASJ_Female Total number of alleles in Ashkenazi Jewish Female called genotypes AN_ASJ_Male Total number of alleles in Ashkenazi Jewish Male called genotypes AN_EAS Total number of alleles in East Asian called genotypes AN_EAS_Female Total number of alleles in East Asian Female called genotypes AN_EAS_Male Total number of alleles in East Asian Male called genotypes AN_Female Total number of alleles in Female called genotypes AN_FIN Total number of alleles in Finnish called genotypes AN_FIN_Female Total number of alleles in Finnish Female called genotypes AN_FIN_Male Total number of alleles in Finnish Male called genotypes AN_Male Total number of alleles in Male called genotypes AN_NFE Total number of alleles in Non-Finnish European called genotypes AN_NFE_Female Total number of alleles in Non-Finnish European Female called genotypes AN_NFE_Male Total number of alleles in Non-Finnish European Male called genotypes AN_OTH Total number of alleles in Other (population not assigned) called genotypes AN_OTH_Female Total number of alleles in Other (population not assigned) Female called genotypes AN_OTH_Male Total number of alleles in Other (population not assigned) Male called genotypes AN_raw Total number of alleles before filtering low-confidence genotypes AN_SAS Total number of alleles in South Asian called genotypes AN_SAS_Female Total number of alleles in South Asian Female called genotypes AN_SAS_Male Total number of alleles in South Asian Male called genotypes BaseQRankSum Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities ClippingRankSum Z-score from Wilcoxon rank sum test of Alt vs. Ref number of hard clipped bases DP Approximate read depth; some reads may have been filtered DP_HIST_ALL Histogram for DP; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 FS Phred-scaled p-value using Fisher's exact test to detect strand bias GQ_HIST_ALL Histogram for GQ; Midpoints of histogram bins: 2.5|7.5|12.5|17.5|22.5|27.5|32.5|37.5|42.5|47.5|52.5|57.5|62.5|67.5|72.5|77.5|82.5|87.5|92.5|97.5 InbreedingCoeff Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation MQ RMS Mapping Quality MQRankSum Z-score from Wilcoxon rank sum test of Alt vs. Ref read mapping qualities QD Variant Confidence/Quality by Depth ReadPosRankSum Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias SOR Symmetric Odds Ratio of 2x2 contingency table to detect strand bias STAR_AC AC of deletions spanning this position STAR_AC_raw Allele counts of deletions spanning this position before filtering low-confidence genotypes STAR_Hemi Count of individuals hemizygous for a deletion spanning this position STAR_Hom Count of individuals homozygous for a deletion spanning this position VQSLOD Log odds ratio of being a true variant versus being false under the trained VQSR gaussian mixture model (deprecated; see AS_RF) VQSR_culprit The annotation which was the worst performing in the VQSR Gaussian mixture model (deprecated; see AS_RF) ClinVar: AF_ESP allele frequencies from GO-ESP AF_EXAC allele frequencies from ExAC AF_TGP allele frequencies from TGP ALLELEID the ClinVar Allele ID CLNVC Variant type CLNVCSO Sequence Ontology id for variant type GENEINFO Gene(s) for the variant reported as gene symbol:gene id SSR Variant Suspect Reason Codes aphid: END Stop position of the interval ExcessHet Phred-scaled p-value for exact test of excess heterozygosity HaplotypeScore Consistency of the site with at most two segregating haplotypes MIN_DP Minimum DP observed within the GVCF block PGT Physical phasing haplotype information, describing how the alternate alleles are phased in relation to one another PID Physical phasing ID information, where each unique ID within a given sample (but not across samples) connects records within a phasing group QD Variant Confidence/Quality by Depth RAW_MQ Raw data for RMS Mapping Quality RGQ Unconditional reference genotype confidence, encoded as a phred quality -10*log10 p(genotype call is wrong) celegans: BQB Mann-Whitney U test of Base Quality Bias (bigger is better) HOB Bias in the number of HOMs number (smaller is better) ICB Inbreeding Coefficient Binomial test (bigger is better) IDV Maximum number of reads supporting an indel IMF Maximum fraction of reads supporting an indel MQ0F Fraction of MQ0 reads (smaller is better) MQB Mann-Whitney U test of Mapping Quality Bias (bigger is better) MQSB Mann-Whitney U test of Mapping Quality vs Strand Bias (bigger is better) NS Number of samples with data RPB Mann-Whitney U test of Read Position Bias (bigger is better) SGB Segregation based metric. VDB Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)" Version="3 phastcons calculated by self of overlapping values in column 4 from phastcons.bed.gz phylop calculated by self of overlapping values in column 4 from phylop.bed.gz FT Genotype-level filter GT Genotype HP Flag used to mark whether a variant was polarized SP Phred-scaled strand bias P-value with Number=0 ============= aphid: ID=DS Type=Flag Were any of the samples downsampled? with Number=4 ============= aphid: SB Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias celegans: DP4 Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases with Number=. (not specified - associate all values with all alleles) ============= gnomAD: AS_RF_POSITIVE_TRAIN Contains the indices of all alleles used as positive examples during training of random forests AS_RF_NEGATIVE_TRAIN Contains the indices of all alleles used as negative examples during training of random forests CSQ Consequence annotations from Ensembl VEP ClinVar: CLNDN ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB CLNDNINCL For included Variant : ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB CLNDISDB Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN CLNDISDBINCL For included Variant: Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN CLNHGVS Top-level (primary assembly, alt, or patch) HGVS expression. CLNREVSTAT ClinVar review status for the Variation ID CLNSIG Clinical significance for this single variant CLNSIGCONF Conflicting clinical significance for this single variant CLNSIGINCL Clinical significance for a haplotype or genotype that includes this variant CLNVI the variant's clinical sources reported as tag-value pairs of database and variant identifier DBVARID nsv accessions from dbVar for the variant MC comma separated list of molecular consequence in the form of Sequence Ontology ID|molecular_consequence ORIGIN Allele origin RS dbSNP ID (i.e. rs number) celegans: ANN Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | ...etc... LOF Predicted loss of function effects for this variant. Format: 'Gene_Name | Gene_ID | etc NMD Predicted nonsense mediated decay effects for this variant. Format: 'Gene_Name | Gene_ID | etc