Schema for Denisova Variants - Variant Calls from High-Coverage Genome Sequence of an Archaic Denisovan Individual
  Database: hg19    Primary Table: dhcVcfDenisovaPinky
VCF File: /gbdb/hg19/bbi/DenisovaPinky.vcf.gz
Format description: The fields of a Variant Call Format data line
See the Variant Call Format specification for more details
chromAn identifier from the reference genome
posThe reference position, with the 1st base having position 1
idSemi-colon separated list of unique identifiers where available
refReference base(s)
altComma separated list of alternate non-reference alleles called on at least one of the samples
qualPhred-scaled quality score for the assertion made in ALT. i.e. give -10log_10 prob(call in ALT is wrong)
filterPASS if this position has passed all filters. Otherwise, a semicolon-separated list of codes for filters that fail
infoAdditional information encoded as a semicolon-separated series of short keys with optional comma-separated values
formatIf genotype columns are specified in header, a semicolon-separated list of of short keys starting with GT
genotypesIf genotype columns are specified in header, a tab-separated set of genotype column values; each value is a colon-separated list of values corresponding to keys in the format column

Sample Rows
1060839.GA428.61.AC=1;AF=0.50;AN=2;BaseQRankSum=-0.424;DP=60;Dels=0.00;FS=0.000;HRun=3;HaplotypeScore=1.8874;MQ=20.06;MQ0=12;MQRankSum=-0.134;QD= ...GT:DP:GQ:PL:A:C:G:T:IR0/1:60:99:459,0,545:17,13:0,0:16,14:0,0:0
1061846.CTC35.22.AC=1;AF=0.50;AN=2;BaseQRankSum=2.604;DP=30;FS=7.650;HRun=12;HaplotypeScore=66.5191;MQ=32.67;MQ0=6;MQRankSum=1.715;QD=1.17;ReadPo ...GT:DP:GQ:PL:A:C:G:T:IR0/1:24:74.25:74,0,447:0,0:13,17:0,0:0,0:7
1067177.CA373.29LowQualAC=1;AF=0.50;AN=2;BaseQRankSum=2.295;DP=20;Dels=0.00;FS=5.119;HRun=13;HaplotypeScore=1.9931;MQ=31.67;MQ0=2;MQRankSum=1.171;QD=18 ...GT:DP:GQ:PL:A:C:G:T:IR0/1:20:7.24:403,0,7:3,9:8,0:0,0:0,0:0
1067220.AG12.14LowQualAC=1;AF=0.50;AN=2;BaseQRankSum=0.198;DP=8;Dels=0.00;HRun=0;HaplotypeScore=0.0000;MQ=33.06;MQ0=1;MQRankSum=-0.922;QD=1.52;ReadPos ...GT:DP:GQ:PL:A:C:G:T:IR0/1:8:41.86:42,0,167:3,3:0,0:0,2:0,0:0
1067391.AG31.21.AC=1;AF=0.50;AN=2;BaseQRankSum=-0.925;DP=59;Dels=0.00;FS=0.000;HRun=1;HaplotypeScore=0.9997;MQ=15.86;MQ0=47;MQRankSum=-0.185;QD= ...GT:DP:GQ:PL:A:C:G:T:IR0/1:59:61.20:61,0,295:18,32:0,0:3,6:0,0:0

Denisova Variants (dhcVcfDenisovaPinky) Track Description
Denisova cave
Denisova cave entrance in the Altai Mountains of Siberia, Russia where the bones were found from which DNA was sequenced (Copyright (C) 2010, Johannes Krause)


The Denisova Variants track shows variant calls made using high-coverage sequence reads from an archaic Denisovan individual mapped to the human genome reference assembly. The Denisova DNA was extracted from a phalanx bone excavated from Denisova Cave in the Altai Mountains in southern Siberia.


A novel single-stranded DNA library preparation method (Meyer, 2012) was applied to DNA previously extracted from 40mg of bone (Reich, 2010). Using single-stranded DNA greatly increased the genomic coverage to 30X compared to an earlier 1.9X sequence (Reich, 2010). Sequence reads were aligned to human sequence Feb. 2009 (GRCh37/hg19) (downloaded from the 1000 Genomes Project) using the Burrows-Wheeler Aligner. Genotype calls for single nucleotide variants and small insertions and deletions were made using the Unified Genotyper from the Genome Analysis Toolkit (GATK), with an additional iteration using a modified reference genome in order to reduce reference bias (Note 6, supplementary online materials of Meyer, 2012).

Variant Call Format (VCF) files were enhanced by adding information from Ensembl Compara EPO alignments of 6 primates and of 35 Eutherian mammals, phastCons conservation scores generated using EPO alignments, 1000 Genomes Project integrated variant call files, University of Washington background selection scores, ENCODE/Duke Uniqueness of 20mers (see the Mappability track), segmental duplications from the Eichler lab (see the Segmental Dups track), and samtools mpileup summaries of mapped reads.

Comprehensive VCF files that include information for homozygous-reference bases and uncovered bases are available. This track uses VCF files that were filtered to retain only those locations that clearly differ from the human reference genome. Reference genome bases without variant calls may indicate either matching Denisova sequence or insufficient data.


Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the variant-only VCF files used for this track.


Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C et al. A high-coverage genome sequence from an archaic Denisovan individual. Science. 2012 Oct 12;338(6104):222-6. PMID: 22936568; PMC: PMC3617501; supplementary online materials, Note 2

Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PL et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468(7327):1053-60. PMID: 21179161