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
| Â | 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%) | |