Description

This track displays regions of the reference genome that have anomalies in the 1000 Genomes Project's mapping of high-throughput sequencing reads from the pilot study of ~180 genomes, each sequenced at low coverage (~2X), from the CEU (CEPH - Northern European from Utah), CHB/JPT (Chinese from Beijing and Japanese from Tokyo) and YRI (Yoruba from Ibadan, Nigeria) populations (see Coriell Institute's description of 1000 Genomes samples). These regions were excluded from the 1000 Genomes Project's SNP-calling process.

Regions with abnormal read depth (total depth is greater than twice the average depth at HapMap3 sites) are displayed in dark red. Regions with low mapping quality (more than 20% of reads from Illumina platform have mapping quality 0) are displayed in light red. Regions with no coverage (no reads mapped) are shown in light gray. There is a separate subtrack per population and type of anomaly.

Methods

Pseudo-fasta files included in the July 2010 release of 1000 Genomes pilot data, containing a mapping code letter for each base in the reference genome, were downloaded from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/other_data/ and processed by UCSC to extract genomic coordinates of annotated regions.

Excerpted from ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/release/2010_07/low_coverage/other_data/README.2010_03.low_coverage_masks:

This directory contains information about the coverage of each base in
the genome in the pilot 1 populations, and whether that base would
have passed the filters used for SNP calling in the consensus released
SNP sets.

The .mask.fa files are pseudo-fasta files for the whole genome,
with instead of a sequence of bases a sequence of the following symbols:
  N  N in reference
  -  no coverage
  M  failed MAPQ0 filter: more than 20% of Illumina reads have mapping quality 0
  D  failed DEPTH filter: total depth is greater than twice the average depth at 
     HapMap3 sites, i.e. >625 for CEU, >445 for YRI, >330 for CHBJPT
  B  failed both M and D filters
  0  passes filters

Note that the filters are relatively conservative, designed to achieve
a false discovery rate below 5%

Bases with D or B are included in the Abnormal Depth subtracks; bases with M or B are included in the Mapping Quality Failure subtracks; and bases with - are included in the No Coverage subtracks.

Credits

Thanks to Richard Durbin, Sendu Bala and the rest of the 1000 Genomes Project Consortium for these data.

References

1000 Genomes Project, http://1000genomes.org/, accessed Sep. 2010.