Table 1

Summary of 454 whole genome sequencing output and SNP identification of a type II/III recombinant T. gondii strain

Number

Chromosome length (bp)

Number of reads*

Total contig length (bp)

Coverage by contigs

Average reads/kb

Type II SNPs* (Green)

Type III SNPs(Blue)

Novel SNPs§ (Orange)

Major SNPdensity/kb

Minor SNP¥ density/kb


Ia

1,896,408

20,649

1,585,140

83.59%

13.03

2

128

7

0.067

0.005

Ib

1,956,324

20,583

1,639,876

83.82%

12.55

1

1,483

10

0.758

0.006

II

2,302,931

24,968

1,939,495

84.22%

12.87

4,370

73

52

1.898

0.054

III

2,470,845

26,771

2,060,909

83.41%

12.99

27

4,224

73

1.710

0.040

IV

2,576,468

27,510

2,150,897

83.48%

12.79

4,731

176

60

1.836

0.092

V

3,147,601

33,619

2,582,080

82.03%

13.02

54

5,725

26

1.819

0.025

VI

3,600,655

39,723

3,042,491

84.50%

13.06

1,985

168

99

0.551

0.074

VIIa

4,502,211

48,365

3,797,608

84.35%

12.74

8,663

79

56

1.924

0.030

VIIb

5,023,822

53,768

4,231,651

84.23%

12.71

62

5,530

41

1.101

0.021

VIII

6,923,375

75,308

5,851,305

84.52%

12.87

123

6,775

158

0.979

0.041

IX

6,384,456

72,298

5,337,365

83.60%

13.55

8,119

325

269

1.272

0.093

X

7,418,475

85,205

6,298,377

84.90%

13.53

13,459

236

209

1.814

0.060

XI

6,570,290

70,653

5,549,592

84.46%

12.73

49

60

117

-

0.034

XII

6,871,637

74,458

5,770,139

83.97%

12.90

58

4,809

75

0.700

0.019

Total

61,645,498

673,878

51,836,925

84.09%

13.00

41,703

29,791

1,252

1.264

0.042


*SNPs denoting a type II background. TgCkUg2 is identical to Me49, but different from VEG. The colors correspond to the colours used for the respective SNP types in Figures 1 and 2 and Additional data files 1 and 2. SNPs denoting a type III background. TgCkUg2 is identical to VEG, but different from Me49. §SNPs where TgCkUg2 has a novel allele, different from both Me49 and VEG. The predominant SNP type, corresponding to the chromosomal background type. ¥SNPs where TgCkUg2 differs from the background type, including novel SNPs.

Bontell et al. Genome Biology 2009 10:R53   doi:10.1186/gb-2009-10-5-r53

Open Data