Mod Hum Variants Track Settings
 
Variant Calls from 11 Modern Human Genome Sequences   (All Denisova Assembly and Analysis tracks)

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 Dinka Variants  Dinka Individual Variant Calls   schema 
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 Mbuti Variants  Mbuti Individual (HGDP00456) Variant Calls   schema 
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 French Variants  French Individual (HGDP00521) Variant Calls   schema 
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 Papuan Variants  Papuan Individual (HGDP00542) Variant Calls   schema 
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 Sardin. Variants  Sardinian Individual (HGDP00665) Variant Calls   schema 
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 Han Variants  Han Individual (HGDP00778) Variant Calls   schema 
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 Yoruba Variants  Yoruba Individual (HGDP00927) Variant Calls   schema 
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 Karit. Variants  Karitiana Individual (HGDP00998) Variant Calls   schema 
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 San Variants  San Individual (HGDP01029) Variant Calls   schema 
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 Mandenka Variants  Mandenka Individual (HGDP01284) Variant Calls   schema 
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 Dai Variants  Dai Individual (HGDP01307) Variant Calls   schema 
    

Description

The Modern Human Variants track shows variant calls made from sequence reads of eleven individuals mapped to the human genome. The purpose of this track is to put the divergence of the Denisova genome into perspective with regard to present-day humans.

Methods

DNA was obtained for each of ten individuals from the CEPH-Human Genome Diversity Panel (HGDP):

  • HGDP00456 (Mbuti)
  • HGDP00521 (French)
  • HGDP00542 (Papuan)
  • HGDP00665 (Sardinian)
  • HGDP00778 (Han)
  • HGDP00927 (Yoruba)
  • HGDP00998 (Karitiana)
  • HGDP01029 (San)
  • HGDP01284 (Mandenka)
  • HGDP01307 (Dai)
DNA was also extracted from a Dinka individual from Sudan (DNK02). To minimize biases due to instrument variability, the samples were pooled for sequencing, using four barcoded libraries per sample. The paired-end reads were aligned to the human genome using the Burrows-Wheeler Aligner and potential PCR duplicates were filtered using Picard.

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.

Credits

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

References

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 Aug 31. [Epub ahead of print] supplementary online materials, Note 6