Denisova Seq Track Settings
 
Denisova High-Coverage Sequence Reads   (All Denisova Assembly and Analysis tracks)

Display mode:      Duplicate track

Display read names
Attempt to join paired end reads by name
Minimum alignment quality:

Color track by bases: Help on base coloring

Alignment Gap/Insertion Display Options Help on display options
Draw double horizontal lines when both genome and query have an insertion
Draw a vertical purple line for an insertion at the beginning or end of the
query, orange for insertion in the middle of the query
Draw a vertical green line where query has a polyA tail insertion

Additional coloring modes:
Color by strand (blue for +, red for -)
Use gray for
No additional coloring

Display data as a density graph:

BAM configuration help

Data schema/format description and download
Assembly: Human Feb. 2009 (GRCh37/hg19)
Data last updated at UCSC: 2012-09-10
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)

Description

The Denisova Sequence track shows 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.

Methods

A novel single-stranded DNA library preparation method (Note 2, supplementary online materials of 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.

Credits

Thanks to the Max Planck Institute for Evolutionary Anthropology for providing the BAM 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 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