Skip to main content

Advertisement

Table 1 Sequence coverage and putative SNPs detected in 14 rhesus macaques ( Macaca mulatta ) and 14 humans ( Homo sapiens ) using parallel methods in a genic-enriched target region

From: The rhesus macaque is three times as diverse but more closely equivalent in damaging coding variation as compared to the human

  Human Macaque
Genome size in reference assembly (Mb) 3,080 2,864
Non-gap reference genome size (Mb) 2,858 2,647
Unique coding sequence size in reference (Mb) 32.5 31.8
Sample number 14 14
Average 36-base reads per sample 17.4 x 106 14.4 x 106
Total length (Mb) of uniquely mapped reads 8,770 7,266
Mb in genome with (≥1x sequence coverage) 1,505 1,571
Mb in genome with (≥3x sequence coverage) 426 435
SNPs in dbSNP_B 131 23,653,737 7,880
SNPs in this study 230,028 462,802
      Also in dbSNP_B131 206,267(89.7%) 34(0.0%)
      Transition AG,GA,TC,CT 155,836(67.7%) 312,643(67.4%)
      Transversion AC,CA,TG,GT 37,046(16.1%) 79,061(17.1%)
      Transversion CG,GC 25,467(11.1%) 46,820(10.1%)
      Transversion AT,TA 11,679(5.1%) 24,857(5.4%)
      Genes with SNPs 14,675 16,797
      Genes with SNPs in exons 11,200 12,466
      SNPs located in intergenic regions 107,461(46.7%) 269,390(58.2%)
      SNPs located in 5Kb upstream of TSS 10,036(4.4%) 26,303(5.7%)
      SNPs located in UTR 18,432(8.0%) 15,455(3.3%)
      SNPs located in intron 79,875(34.7%) 130,443(28.2%)
      SNPs located in CDS 14,224(6.2%) 21,211(4.6%)
        Synonymous 8,329(58.6%) 13,798(65.1%)
        Non-synonymous 5,877(41.3%) 7,367(34.7%)
           Damaging* 1,741 (29.6%) 1,525 (20.7%)
        Nonsense 18(0.1%) 46(0.2%)
  1. *damaging as evaluated by Polyphen.