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Description

The Modern Human Seq track shows human sequence reads of five individuals mapped to the human genome. The purpose of this track is to put the divergence of the Neandertal genomes into perspective with regard to present-day humans.

Display Conventions and Configuration

The sequence reads (query sequences) from each of the five individuals are contained in separate subtracks. Use the checkboxes to select which individuals will be displayed in the browser. Click and drag the sample name to reorder the subtracks. The order in which the subtracks appear in the subtrack list will be the order in which they display in the browser.

The query sequences in the SAM/BAM alignment representation are normalized to the + strand of the reference genome (see the SAM Format Specification for more information on the SAM/BAM file format). If a query sequence was originally the reverse of what has been stored and aligned, it will have the following flag:

 (0x10) Read is on '-' strand.
 

BAM/SAM alignment representations also have tags. Some tags are predefined and others (those beginning with X, Y or Z) are defined by the aligner or data submitter. The following is a list of the tags associated with this track. For this track, those starting with X are specific to the Burrows-Wheeler Aligner (BWA).

The item labels and display colors of features within this track can be configured through the controls at the top of the track description page.

Methods

The genomes of a San individual from Southern Africa (HGDP01029), a Yoruba individual from West Africa (HGDP00927), a Han Chinese individual (HGDP00778), an individual from Papua New Guinea (HGDP00542), and a French individual (HGDP00521) from Western Europe were sequenced to 4- to 6-fold coverage on the Illumina GAII platform. These sequences were aligned to the human reference genome (NCBI36/hg18) using the Burrows-Wheeler Aligner (BWA). Reads with an alignment quality of less than 30 were not included in these data. Those with an alignment quality greater than or equal to 30 were analyzed using a similar approach to that used for the Neandertal data.

Credits

This track was produced at UCSC using data generated by Ed Green.

References

Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH et al. -A Draft Sequence of the Neandertal Genome. Science. 2010 7 May;328(5979):710-22.

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics. 2009 Jul 15;25(14):1754-60.