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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 (%)	R[ii] ×10⁻⁹
Human–Chimpanzee
Overall	51	4968069	4853708	4798947	54761	36914	17847	2.07	98.87 ± 0.00	1.14 ± 0.00[iii]	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 ± 0.01[iii]	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 ± 0.08[iii]	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

[i] 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).

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

[iii] 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).