Skip to main content

Table 3 Basic assembly statistics for various read mixes

From: Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes

454 Read Mix1

Scaffolds

total

Scaffolds

anchored

Scaffold Length (bp)

Anchored Length (%)

Match Score2

Relocation Score2

Inversion Score2

Coverage Score2

Gap Length (%N)

Subgenome length (bp)

35L-20PP

16

5

2,925,652

96.5%

0.64

1.00

1.00

0.93

0.05%

3,032,287

20PP-20NM

23

5

2,948,378

95.6%

0.59

1.00

1.00

0.93

0.23%

3,085,172

10PP-10NM

20

9

2,919,380

96.1%

0.57

0.99

0.89

0.93

0.56%

3,037,466

20L-10PP

15

8

2,848,345

97.0%

0.56

1.00

1.00

0.92

0.88%

2,937,025

20L-15PP

14

7

2,894,304

96.7%

0.56

1.00

1.00

0.93

0.51%

2,993,053

20L-20PP

17

7

2,921,393

96.7%

0.56

1.00

1.00

0.93

0.30%

3,021,076

15PP-15NM

19

6

2,932,591

95.8%

0.55

1.00

1.00

0.93

0.39%

3,060,041

10L-20PP

13

7

2,917,670

96.6%

0.54

1.00

1.00

0.93

0.23%

3,021,711

15L-20PP

12

6

2,910,841

96.7%

0.54

1.00

1.00

0.93

0.29%

3,009,135

5L-20PP

15

6

2,874,297

94.5%

0.54

1.00

1.00

0.93

0.87%

3,040,453

10L-15PP

18

8

2,884,836

96.5%

0.53

1.00

1.00

0.92

0.74%

2,988,073

15L-15PP

15

8

2,892,073

96.7%

0.53

1.00

1.00

0.93

0.61%

2,989,876

5L-15PP

15

7

2,845,042

96.6%

0.53

1.00

1.00

0.92

1.48%

2,945,611

0L-20PP

13

6

2,877,053

94.9%

0.52

1.00

1.00

0.93

0.90%

3,031,950

10L-10PP

19

10

2,835,308

96.0%

0.52

1.00

1.00

0.91

1.02%

2,953,066

15L-10PP

16

8

2,835,593

96.8%

0.52

1.00

1.00

0.91

0.96%

2,928,679

20L-5PP

30

8

2,650,829

87.7%

0.52

0.99

0.94

0.72

2.84%

3,022,574

5L-10PP

25

10

2,734,631

96.2%

0.52

1.00

1.00

0.90

1.54%

2,843,359

0L-10PP

23

9

2,738,500

96.5%

0.51

0.93

0.78

0.90

1.68%

2,838,999

0L-15PP

17

7

2,836,521

94.5%

0.51

1.00

1.00

0.92

1.70%

3,001,136

10L-5PP

42

12

2,491,349

80.5%

0.51

0.89

0.38

0.66

5.20%

3,096,682

15L-5PP

34

9

2,588,122

84.3%

0.51

0.98

0.79

0.66

3.96%

3,068,882

5L-5PP

57

17

2,248,580

75.2%

0.51

0.91

0.62

0.66

7.06%

2,989,391

0L-5PP

57

17

2,214,995

74.7%

0.50

0.90

0.21

0.61

8.84%

2,967,162

35L-0PP

174

35

2,911,931

48.4%

0.50

0.99

0.28

0.51

0.00%

6,013,556

20L-0PP

70

26

1,812,591

59.4%

0.44

1.00

0.06

0.28

0.00%

3,048,991

10L-0PP

41

20

1,033,618

64.5%

0.40

1.00

0.55

0.17

0.00%

1,601,933

15L-0PP

57

23

1,485,809

59.2%

0.40

1.00

0.13

0.14

0.00%

2,510,749

5L-0PP

29

12

631,622

57.4%

0.27

1.00

0.12

0.07

0.00%

1,100,803

  1. 1Number = fold sequencing depth; L = linear (shotgun) reads; PP = true pair reads; NM = Unmated (shotgun) reads.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us