Description

This track shows which genome regions are more or less accessible to next generation sequencing methods that use short, paired-end reads. It summarizes whole genome sequencing data from Phase 1 of the 1000 Genomes Project and shows two levels of stringency: "pilot" stringency regions (see below) cover 94% of non-N bases in the genome and "strict" regions cover 72% of non-N bases. Each site which meets "strict" criteria also passes the "pilot" criteria.

This track does not show a mask of regions in which variant calls can or cannot be made. Some 1000 Genomes Phase 1 variant calls are in regions that do not meet the "strict" criteria. Phase 1 variant calls are filtered using the Variant Quality Score Recalibrator (VQSR) method (implemented in the Genome Analysis Toolkit (GATK)) without regard to the thresholds applied here. VQSR assesses the evidence for variation at sites where there is evidence, but says nothing about the remaining sites.

These regions will be useful for (a) comparing accessibility using current technologies to accessibility in the 1000 Genomes Pilot Project, and (b) population genetic analyses (such as estimates of mutation rate) that must focus on genomic regions with very low false positive and false negative rates.

Methods

The total depth of mapped sequence reads, the average mapping quality score and the fraction of reads with mapping quality zero (meaning that this read maps equally well to more than one location in the genome) are tabulated from 1,103 .bam files in the 1000 Genomes Phase 1 low coverage data release. This combines low coverage whole genome sequence information from 1,092 individuals, giving a genome wide average total depth of coverage of 5,132 reads. Both "pilot" and "strict" tracks are .bed file conversions of the "pass" regions from .fasta mask files. See the Genome Masks README file in that directory for details.

The "pilot" criteria require a depth of coverage between 2,566 and 10,264 inclusive (between one-half and twice the average depth) and that no more than 20% of covering reads have mapping quality zero. These are equivalent to the criteria used for analyses in the 1000 Genomes Pilot paper (2010). The "strict" criteria require a depth of coverage between 2,566 and 7,698 inclusive, no more than 0.1% of reads with mapping quality zero, and an average mapping quality of 56 or greater. This definition is quite stringent and focuses on the most unique regions of the genome. In regions which passed the strict criteria, only ~2% of sites called in an initial analysis were rejected as likely false positives by VQSR. Since approximately one-half of 1000 Genomes Project individuals are males, the depth of coverage is generally lower on the X chromosome. Coverage thresholds on the X chromosome were adjusted by a factor of 3/4 and on the Y chromosome by a factor of 1/2. The "pilot" criteria were not evaluated for the Y chromosome.

1000 Genomes Phase 1 sequencing was done between 2008 and 2010 using Illumina (86.4%), AB SOLiD (13%) and Roche LS 454 (0.6%) sequencing technologies. Of the Illumina coverage, 45% is in approximately 100 bp paired-end reads, 31.5% is in 76 bp reads, 15% is in 51 bp reads and 8.5% is in 36 bp reads. All AB SOLiD data are 50 bp mate paired reads. Paired-end sequence reads were mapped against the GRCh37 human genome reference sequence using BWA version 0.5.5, BFAST version 0.6.4e and SSAHA version 2.5 respectively. Full details are in a README file and in supplementary materials to the Phase 1 paper (2012).

The mapping target consists of the 22 autosomes plus X and Y chromosomes (both pseudo-autosomal regions on the Y are masked by Ns), the revised CRS mitochondrial sequence (NC_012920), and 59 unplaced contigs. It does not include the human herpesvirus 4 sequence (used for cell line transformation) nor approximately 5 Mb of additional "decoy" sequence compiled from other human entries in GenBank. Those sequences were added to the mapping target in July 2011 and will be included in the mapping during 1000 Genomes Phase 2. Full details are in the Human Decoy Sequences README file.

Credits

Mary Kate Trost and Gonçalo Abecasis at the University of Michigan Center for Statistical Genetics generated the original masked fasta files. Tom Blackwell at UM converted those to .bed format and edited the description and methods. Thanks to the 1000 Genomes Project for making Phase 1 data available in advance of publication.

References

1000 Genomes Pilot Project:
1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature. 2010 Oct 28;467(7319):1061-73.

Phase 1 of the 1000 Genomes Project:
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65.

1000 Genomes Frequently Asked Questions (FAQ)