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Table 1 Summary statistics for KhoeSan exomes

From: Exome capture from saliva produces high quality genomic and metagenomic data

   Total readsa Unmapped reads % Un-mapped reads % PCR duplicates % Mapped on target Median target coverageb % of variants coveredc Autosomal SNV Autosomal singletons Non-ref. concordanced
Pilot 1 SA006 69,272,282 9,122,731 13.2% 54.2% 63.5% 12 94.9% 25,225 657 0.9897
  SA008 113,888,276 2,143,408 1.9% 19.8% 78.2% 73 99.5% 26,408 955 0.9947
  SA011 78,006,472 1,664,959 2.1% 33.7% 77.4% 40 99.0% 26,365 67 NA
  SA012 67,209,032 1,353,187 2.0% 20.5% 75.7% 42 99.3% 26,722 86 NA
  SA035 85,142,498 5,812,851 6.8% 78.0% 79.4% 10 92.1% 24,692 1,726 0.9884
  SA051 76,076,464 3,102,819 4.1% 27.8% 76.5% 37 98.8% 27,674 1,239 NA
  SA052 60,375,472 1,247,951 2.1% 12.9% 78.2% 41 98.8% 27,779 755 0.9968
  SA054 62,358,148 1,959,032 3.1% 27.9% 73.9% 31 99.3% 28,024 817 0.9956
  Pilot 1 mean 76,541,081 3,300,867 4.4% 34.4% 75.4% 35.75 97.7% 26,611 788 e 0.9930
Pilot 2 SA1000 77,069,730 8,387,491 10.9% 9.5% 57.3% 44 98.4% 27,921 2,483 0.9915
  SA1001 85,479,934 3,551,500 4.2% 11.4% 74.2% 67 98.7% 27,694 2,318 0.9939
  SA1002 92,542,846 4,674,919 5.1% 15.5% 70.1% 65 98.8% 27,886 3,286 0.9941
  SA1006 83,545,692 4,002,665 4.8% 18.1% 74.5% 59 98.4% 27,446 2,442 0.9927
  SA1010 87,939,484 4,445,502 5.1% 14.5% 71.0% 62 98.6% 27,295 1,782 0.9935
  SA1011 82,377,158 7,810,714 9.5% 11.6% 49.2% 40 98.5% 27,484 2,717 0.9887
  SA1025 81,405,650 2,498,412 3.1% 10.0% 87.8% 63 99.3% 28,696 2,676 0.9934
  Pilot 2 mean 84,337,213 5,053,029 6.1% 12.9% 69.2% 57.14 98.7% 27,775 2,529 0.9925
  1. aTotal number of DNA fragments including: mapped, unmapped and duplicate reads.
  2. bLimited to non-duplicate reads on autosomes, as calculated by GATK Unified Genotype.
  3. cLimited to XX autosomal SNPs identified at the 99% VQSR threshold.
  4. dConcordance at heterozygous and homozygous non-reference positions as compared to Illumina OmniExpress or 550K.v2 SNP arrays.
  5. eFewer average singletons as a result of including closely related individuals in Pilot 1. See Additional file 1: Table S1 for individual data.