Table 2

Alignment and SNP-calling statistics

Strain

Reads^a

c50, c95 cov^b

SNP-able sites^c

SNP

Hom^d

Het^e

Divergence (hom only)^f

HM-1A

13,743,406

35,141

10,012,951

2,217

229

1,988

0.22 (0.02)

HM-1B

9,586,924

26,95

9,819,882

1,995

220

1,775

0.20 (0.02)

Rahman

19,498,380

32,198

9,817,503

6,889

3,767

3,122

0.70 (0.38)

2592100

13,560,609

26,127

10,025,805

6,788

3,128

3,660

0.68 (0.31)

PVBM08B

17,627,870

36,172

10,335,217

7,999

4,225

3,774

0.77 (0.41)

PVBM08F

8,436,907

19,65

10,253,328

6,602

3,613

2,989

0.64 (0.35)

IULA:1092:1

19,041,335

48,155

11,934,434

10,014

4,897

5,117

0.84 (0.41)

HK-9

21,193,087

41,202

10,678,584

9,155

4,428

4,727

0.86 (0.41)

MS84-1373

21,479,273

51,209

10,308,534

8,373

4,027

4,346

0.81 (0.39)

MS27-5030

20,403,218

47,225

8,731,329

7,001

3,302

3,699

0.80 (0.38)

^a'Reads' = the number of uniquely aligned reads. ^b'c50, c95 cov' = the 50th and 95th centile of coverage depth. ^c'SNP-able sites' = positions passing criteria for allowing a SNP to be called (see Materials and methods). ^d'Hom' = homozygous SNP. ^e'Het' = heterozygous SNP. ^f'Divergence (hom only)' = divergence from reference genome (divergence calculated using only homozygous SNPs).

Weedall et al. Genome Biology 2012 13:R38   doi:10.1186/gb-2012-13-5-r38