Table 3 Nucleotide variation in assemblies to human

From: Expanding whole exome resequencing into non-human primates

	Chimpanzee						Rhesus macaque
	Sample			Genome			Sample			Genome
	Hom	Het	Hemi	Hom	Het*	Hemi	Hom	Het	Hemi	Hom	Het*	Hemi
Deletions
Frameshift	147	185	11	550	296	72	337	360	18	504	200	32
Amino acid loss	191	210	12	183	74	10	643	295	35	697	290	37
Insertions
Frameshift	104	163	11	242	260	29	190	321	15	281	300	17
Amino acid gain	109	269	13	69	237	3	319	600	27	246	755	34
MNP
Synonymous	289	125	10	78	13	4	1,310	318	81	963	52	41
Non-synonymous	1,986	1,024	56	1,971	293	79	13,022	2,822	502	17,762	982	682
Stop codon gain	7	27	1	20	16	4	36	106	1	55	28	0
Stop codon loss	2	2	0	0	2	0	8	4	0	6	2	0
SNP
Synonymous	76,204	14,506	2,355	75,930	826	1,864	318,662	23,085	11,117	346,779	2,688	11,653
Non-synonymous	49,699	16,017	2,220	49,093	1,105	1,696	139,476	22,633	5,943	160,418	2,574	6,479
Stop codon gain	204	379	19	228	17	15	400	732	20	445	26	21
Stop codon loss	85	34	4	27	1	3	137	50	5	75	2	3
Genes
Deletion frameshift	143		10	489 (678)^a		55	328		17	438 (579)^a		27
Insertion frameshift	101		10	230 (439)^a		28	180		14	266 (519)^a		16
Either	241		20	679 (1,016)^a		76	489		29	665 (1,013)^a		39
Stop codon gain	200		16	237 (259)^a		14	406		21	443 (494)^a		19
Stop codon loss	87		4	28 (32)^a		0	143		5	80 (84)^a		3
Either	280		19	263 (289)^a		14	534		26	513 (567)^a		22
Any of above	499		39	895 (1,316)^a		87	945		51	1082 (1,425)^a		56

Comparison of nucleotide level variation in sample reads and genomic cross-species alignments to human. ^aValues in parentheses are Hom + Het*. Hemi, hemizygous; Het, heterozygous; Hom, homozygous; MNP, multi-nucleotide polymorphism; SNP, single-nucleotide polymorphism.

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