Table 1

Rice (Oryza sativa ssp. japonica cv. Nipponbare) whole-genome shotgun optical mapping

Ch.

Est. Size (Mb) YACa

Est. Size (Mb) BACb

FISHc Size(Mb)/AR

IRGSPd

Opt. Map Contig (status)

Opt. Map (Mb)

Predicted Size (Mb)e/ArmRatio

Difference (%) YAC/BAC/FISH/IRGSP

Ave. frag. size (kb)

# of Mol.

X Cov.

Ave. frag. size SD (kb)


1

51.5

44

56.9/1.63

45.05

1(F)

43.66

43.73/1.61

17.77/0.62/30.12/3.02

15.86

3,311

40.48

1.44

2

43.4

39.8

48.8/1.68

36.78

1(F)

36.14

36.21/1.62

19.86/9.91/34.77/1.57

15.15

2,456

35.69

1.47

3

47.5

40.8

52.5/0.89

37.37

1(F)

36.97

37.03/0.84

28.27/10.18/41.78/0.92

15.30

2,669

39.38

1.46

4

36.8

39

35.5/5.13

36.15

1(F)

35.80

35.85/2.61

2.65/8.79/0.98/0.84

14.55

2,368

35.38

1.39

5

33.6

33.2

34.6/1.99

30.00

1(F)

30.06

30.11/1.44

11.59/10.26/14.91/0.37

14.30

1,845

33.03

1.40

6

35.1

31.8

35.7/0.93

31.60

1

16.09

31.94/1.01

9.89/0.44/11.77/1.06

13.99

1,536

47.03

1.37

2

15.78

14.89

1,483

44.17

1.40

7

33.1

35

32.3/1.78

30.28

1(F)

29.65

29.71/1.45

11.41/17.81/8.72/1.92

14.41

2,052

35.93

1.37

8

33.6

27.6

30.0/1.38

28.56

1(F)

28.40

28.45/1.09

18.10/2.99/5.45/0.39

13.46

2,244

39.38

1.37

9

27

21.6

26.7/6.54

30.53

1

24.50

26.53/2.77

1.77/18.58/0.64/15.08

14.16

2,112

39.19

1.48

10

23.7

26.8

23.0/3.07

23.96

1(F)

23.96

24.00/1.85

1.25/11.67/4.17/0.17

13.12

2,658

55.74

1.32

11

33.7

30.3

28.8/1.32

30.76

1

17.21

31.00/1.39

8.71/2.26/7.10/0.77

14.34

1,202

35.38

1.34

2

12.37

14.11

931

35.55

1.39

12

30.9

30.6

25.1/1.32

27.77

1(F)

28.19

28.24/1.22

9.42/8.36/11.12/1.66

14.07

2,645

45.38

1.27

Total

430

400.5

430

388.82

14

378.31

382.80/NA

12.33/4.62/12.33/1.57

29,512

Ave.

14.41

40.12

1.39


*Ch. = Chromosome; est. = estimated; AR = Arm Ratio; Opt. = Optical; Ave. = Average; Frag. = Fragment; SD = Standard Deviation; Cov. = Coverage; F = Finished; Difference = |Estimated size-Optical Map size|/Optical Map size*100%; Mol. No.: the number of single molecule maps were used to build the chromosome optical map contig; X Coverage = (total mass of maps within a contig)/(chromosome optical map consensus size). a Estimated chromosome size is based on the YAC and BAC physical map [7]; b Estimated chromosome size is based on the BAC/PAC physical map [13]; c Estimated chromosome size by pachytene FISH [62]. d International Rice Genome Sequencing Project [37]. ePredicted chromosome size = the optical map sizes + gap sizes [the centromere sizes in BAC and YAC map for chromosome 6 and 11] + missing small fragment sizes (Table 2).

Zhou et al. BMC Genomics 2007 8:278   doi:10.1186/1471-2164-8-278

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