Table 3

Nucleotide variation in assemblies to human

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.

Vallender Genome Biology 2011 12:R87   doi:10.1186/gb-2011-12-9-r87

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