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. 2003 Mar 1;13(3):358–368. doi: 10.1101/gr.923303

Table 1.

Primate Single-Nucleotide Variation versus Sequence Class

# loci Alignment length (bp) Aligned bases (bp) Matches (bp) Mismatches (bp) Transitions (s) Transversions (v) s/v Identity (%) Kimura Distance (%) Ra ×10−9
Human–Chimpanzee
 Overall 51 4968069 4853708 4798947 54761 36914 17847 2.07 98.87 ± 0.00 1.14 ± 0.00b 1.034 ± 0.004
 Overall-CG 51 4968069 4764283 4723249 41034 15414 25620 1.66 99.14 ± 0.00 0.87 ± 0.00 0.788 ± 0.004
 Exon 24 69051 68957 68543 414 296 118 2.51 99.40 ± 0.03 0.60 ± 0.03 0.548 ± 0.027
 Unique noncoding 51 2749584 2720023 2692593 27430 8913 18517 2.08 98.99 ± 0.01 1.02 ± 0.01 0.924 ± 0.006
 Repetitive 51 2201336 2098297 2070750 26547 8393 18154 2.16 98.73 ± 0.01 1.28 ± 0.01 1.162 ± 0.007
  Alu 51 446212 419379 412882 6497 4577 1920 2.38 98.45 ± 0.02 1.57 ± 0.02 1.425 ± 0.018
  Alu-CG 51 446212 399048 395013 4035 1567 2468 1.57 98.99 ± 0.02 1.02 ± 0.02 0.926 ± 0.015
  L1 51 837035 767774 758213 9561 6322 3239 1.95 98.75 ± 0.01 1.26 ± 0.01 1.143 ± 0.012
Human–Baboon
 Overall 42 4984965 4456507 4204745 251762 167380 84382 1.98 94.35 ± 0.01 5.90 ± 0.01b 1.181 ± 0.002
 Overall-CG 42 4984965 4351198 4140103 211095 75237 135858 1.81 95.15 ± 0.01 5.03 ± 0.01 1.007 ± 0.002
 Exon 24 48578 48098 46627 1471 1042 429 2.43 96.94 ± 0.08 3.13 ± 0.08 0.627 ± 0.016
 Unique noncoding 42 3148255 3022715 2862848 159867 106002 53865 1.97 94.71 ± 0.01 5.51 ± 0.01 1.102 ± 0.003
 Repetitive 42 1973097 1555295 1456755 98540 66258 32282 2.05 93.66 ± 0.02 6.66 ± 0.02 1.332 ± 0.004
  Alu 42 404917 292641 267869 24772 17219 7553 2.28 91.54 ± 0.05 9.07 ± 0.06 1.814 ± 0.012
  Alu-CG 42 404917 275514 256962 18552 6506 12046 1.85 93.27 ± 0.05 7.10 ± 0.05 1.419 ± 0.011
  L1 42 778575 538863 507237 31626 20465 11161 1.83 94.13 ± 0.03 6.14 ± 0.04 1.228 ± 0.007
Human–Lemur
 Overall 9 623139 423139 341061 82078 47053 35025 1.34 80.60 ± 0.06 22.73 ± 0.08b 2.066 ± 0.008
 Overall-CG 9 623139 406011 332321 73690 31863 41827 1.31 81.85 ± 0.06 21.01 ± 0.08 1.910 ± 0.007
 Unique 9 370337 313512 255977 57535 33526 24009 1.40 81.65 ± 0.07 21.31 ± 0.09 1.938 ± 0.009
 Repetitive 9 244728 103787 80333 23454 12909 10545 1.22 77.40 ± 0.13 27.25 ± 0.19 2.477 ± 0.017

Orthologous sequences were globally aligned with ALIGN (Methods). A suboptimal alignment was defined as any alignment which exceeded two standard deviations of the mean genetic distance (window size 2 kb, slide 100 bp). These regions were not included in the analysis. The mean and standard deviation of alignment lengths are 106, 107 ± 41,659, 95,171 ± 38,751, and 47,015 ± 34,144 bp for human–chimpanzee, human–baboon, and human–lemur comparisons. Exon sequence was restricted only to well-annotated human genes (NCBI RefSeq database). Repetitive sequences were detected using RepeatMasker (version 3.0). Unique noncoding regions excluded both exonic and repetitive regions. For human–baboon and human–chimpanzee comparisons, Alu and L1 were calculated separately. Relatively few L1 and Alu repeats were orthologous between human and lemur genomic alignments and were therefore not partitioned. Due to the enrichment of CpG dinucleotides with Alu repeats, we considered substitutions without CpG dinucleotides (Alu-CG) as well as the overall content minus CpG dinucleotides in each species (Overall-CpG).

a

Substitution rate calculations assume divergence times of the human lineage from chimpanzee, baboon and lemur of 5.5, 25 and 55 Mya (Goodman 1999).

b

If suboptimal alignments were included in the analysis, the overall genetic distance increases to 1.14 ± 0.00%, 6.05 ± 0.01% and 25.69 ± 0.07%, respectively (Methods).