Table 1

Purple Kush sequencing library statistics

Library

Insert size (bp)

Raw No.

Raw nt (Gb)

Filtered No.

Filtered nt (Gb)

% in a) assembly


Genomic DNA, Illumina 2 × 100 bp paired-end reads

CS-PK_SIL-1a

181

143,951,601

28.0

124,499,863

23.8

82.2

CS-PK_SIL-1b

195

111,106,936

22.2

98,124,711

19.0

82.4

CS-PK_SIL-2a

313

93,774,355

18.8

81,421,333

15.3

84.7

CS-PK_SIL-3b

362

66,932,319

13.4

60,519,955

11.6

82.8

CS-PK_SIL-B

664

95,648,778

19.1

49,550,098

9.2

85.1

CS-PK_SIL-C

580

101,329,142

20.3

72,977,620

13.6

87.1

Genomic DNA, Illumina 2 × 44 bp mate pair reads

CS-PK_2 kb-1a

1,926

36,057,086

3.2

24,688,690

2.2

75.0

CS-PK_2 kb-1b

1,846

32,385,628

2.8

24,405,458

2.1

76.8

CS-PK_2 kb-2a

1,850

37,761,064

3.3

29,927,921

2.6

75.5

CS-PK_2 kb-2b

1,787

37,111,622

3.3

28,744,604

2.5

77.1

CS-PK_5 kb-1

4,721

36,182,230

3.2

27,377,398

2.4

77.5

CS-PK_5 kb-2

4,585

64,613,144

5.7

50,712,974

4.4

79.9

Genomic DNA, 454 mate pairs

CS-PK_8 kb-1

8,000

557,443

0.20

192,483

0.069

77.0

CS-PK_8 kb-2

8,000

484,033

0.17

176,405

0.063

74.5

CS-PK_8 kb-3

8,000

603,780

0.21

221,616

0.079

78.6

CS-PK_13 kb-1

13,000

430,642

0.11

96,503

0.030

75.1

CS-PK_20 kb-1

20,000

611,986

0.19

216,379

0.070

77.0

CS-PK_20 kb-2

20,000

575,618

0.21

228,811

0.081

77.0

CS-PK_30 kb-1

30,000

644,026

0.22

239,625

0.082

72.8

CS-PK_30 kb-2

30,000

536,273

0.15

150,510

0.048

73.4

CS-PK_40 kb-1

40,000

213,928

0.06

64,325

0.019

74.9

CS-PK_40 kb-2

40,000

627,945

0.21

241,189

0.079

76.8

CS-PK_40 kb-3

40,000

573,313

0.19

224,264

0.073

74.5

RNA, Illumina 1 × 100 bp single-end reads

PK-Mid-flower

-

37,835,287

3.8

25,687,331

2.3

-

PK-Early-flower

-

37,472,665

3.7

25,434,724

2.3

-

PK-Pre-flower

-

54,026,640

5.4

35,522,980

3.2

-

PK-Shoot

-

55,653,984

5.6

36,204,828

3.3

-

PK-Stem

-

60,353,149

6.0

39,274,463

3.5

-

PK-Root

-

37,374,640

3.7

24,904,927

2.2

-

RNA, Illumina 2 × 100 bp paired-end reads

PK-subtracted1

180

110,483,894

22.1

64,525,082

11.6

-

PK-subtracted2

180

82,190,044

16.4

46,291,148

8.3

-

PK-subtracted3

180

105,737,119

21.1

61,974,962

11.2

-

PK-subtracted4

180

48,599,953

9.7

26,505,457

4.8

-


a) Percentage of genomic DNA reads that could be mapped back to the canSat3 genome assembly

van Bakel et al. Genome Biology 2011 12:R102   doi:10.1186/gb-2011-12-10-r102

Open Data