Modern Human Seq Track Settings
 
Alignments of Sequence Reads from 7 Humans   (All Denisova Assembly and Analysis tracks)

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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 -)
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No additional coloring

Display data as a density graph:

BAM configuration help

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  Sample↓1   Track Name↓2  
 
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 Mbuti Pygmy  Mbuti Pygmy (HGDP00456) Sequence Reads   Schema 
 
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 Melanesian  Melanesian (HGDP00491) Sequence Reads   Schema 
 
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 Papuan  Papuan (HGDP00551) Sequence Reads   Schema 
 
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 Sardinian  Sardinian (HGDP00665) Sequence Reads   Schema 
 
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 Cambodian  Cambodian (HGDP00711) Sequence Reads   Schema 
 
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 Native Americans  Native American (HGDP00998) Sequence Reads   Schema 
 
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 Mongolian  Mongolian (HGDP01224) Sequence Reads   Schema 
    

Description

The Modern Human Seq track shows human sequence reads of seven 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 seven individuals from the CEPH-Human Genome Diversity Panel (HGDP): HGDP00456 (Mbuti), HGDP00998 (Karitiana Native American), HGDP00665 (Sardinia), HGDP00491 (Bougainville Melanesian), HGDP00711 (Cambodian), HGDP01224 (Mongolian) and HGDP00551 (Papuan). Each library was sequenced on the Illumina Genome Analyzer IIx using 2x101 + 7 cycles on one flow cell according to the manufacturer's instructions for multiplex sequencing. The paired-end reads were aligned using the Burrows-Wheeler Aligner to the human sequence (NCBI36/hg18)

Download the Modern Human Seq track data sets from the Genome Browser downloads server.

References

Briggs A.W., Stenzel U., Meyer M., Krause J., Kircher M., Pääbo S. Removal of deaminated cytosines and detection of in vivo methylation in ancient DNA. Nucleic Acids Res. 2009 Dec 22:38(6) e87.

Reich D., Green R.E., Kircher M., Krause J., Patterson N., Durand E.Y., Viola B., Briggs A.W., Stenzel U., Johnson P.L.F. et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature. 2010 Dec 23;468:1053-1060.

Credits

This track was produced at UCSC using data generated by the Max Planck Institute for Evolutionary Anthropology.