Table 1

Coverage of the Nipponbare Pseudomolecules 4.0 database by the Koshihikari reads from the Solexa Genome Analyzer.

Uniquely mapped reads


Chromosome

Pseudomolecule of Nipponbare (bp)a

Koshihikari aligned length (bp)b

Coverage (%)

Total number

bp

Total number of mapped contigs

Sequencing depth (fold)

Total of SNPs


1

45,064,769

36,886,997

81.9

21,887,208

719,138,056

63,889

16.6

10,980

2

36,823,111

31,152,504

84.6

19,972,645

656,243,813

53,822

18.3

4,113

3

37,257,345

32,175,988

86.4

19,309,856

634,463,329

51,236

17.5

2,773

4

35,863,200

27,331,878

76.2

15,718,358

516,454,041

69,662

14.6

9,891

5

30,039,014

24,458,877

81.4

14,277,427

469,092,491

51,892

15.7

1,032

6

32,124,789

25,763,900

80.2

14,992,102

492,566,411

53,317

15.8

1,165

7

30,357,780

24,230,102

79.8

13,935,933

457,866,127

55,090

15.4

7,561

8

28,530,027

22,970,652

80.5

13,106,335

430,601,662

53,667

15.2

6,426

9

23,843,360

19,060,074

79.9

11,008,304

361,678,832

41,137

15.7

178

10

23,661,561

18,592,212

78.6

10,572,960

347,371,203

43,569

15.3

3,617

11

30,828,668

22,439,806

72.8

12,582,930

413,402,408

58,282

14.5

12,216

12

27,757,321

21,114,982

76.1

11,932,390

392,027,726

58,990

14.1

7,099


Total or averagec

382,150,945

306,177,972

80.1d

179,296,448

5,890,906,099

654,543

15.7

67,051


a IRGSP, pseudomolecule build4

bTotal length of aligned base except for unidentified base 'N'.

cTotal number except the column of coverage and sequencing depth, these are discribed as average value.

dCoverage is calcurated based on Koshihikari aligned length/Pseudomolecule of Nipponbare. The value is slightly different from average of coverage of respective chromosome.

Yamamoto et al. BMC Genomics 2010 11:267   doi:10.1186/1471-2164-11-267

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