Table 3

Comparison between the optical maps and the in silico maps from the TIGR pseudomolecules of rice genome sequence

TIGR sequence pseudomolecule

Optical Map

Ch.

# Match frag.

Total match frag. mass (Mb)

Percent (%) out of total mass^a

Ave. frag. relative sizing error(%)

# Telomeric gap/mass (kb)

Centr. gap mass (kb)

# Gaps Filling/Mass (kb)

# Gaps Calling/mass (kb)

# Misassembly/Mass (kb)

# Missing small frag./mass (kb)

# Missing/false cut(s)

1

2641

42.94

98.35

3.32

2/14

1/795

6/69

6/42

3/328

69/57.60

44/4

2

2301

35.52

98.28

3.45

1/10

1/466

3/17

2/12

2/14

62/52.53

33/1

3

2261

35.93

97.19

3.46

2/37

1/432

4/496

6/67

1/7.5

74/63.56

45/4

4

2279

34.63

96.73

3.57

2/112

0/0

3/65

21/621

11/435

62/51.92

36/5

5

2005

29.48

98.07

3.65

2/255

1/77

4/60

8/62

5/250

56/47.05

34/4

6

2118

30.90

96.74

3.31

2/175

1/810

1/2

3/17

1/42

73/61.90

39/4

7

1977

29.38

99.09

3.64

2/20

1/61

1/23

8/146

2/30

54/48.19

48/5

8

2009

28.10

98.94

3.49

2/23

1/24

1/1

8/245

2/68

52/45.18

37/2

9

1625

22.56

85.20

3.73

2/3451

1/302

4/54

3/20

2/57

58/52.50

42/4

10

1683

22.52

93.99

3.34

2/51

1/402

6/498

6/76

1/9

43/34.02

28/4

11

1939

28.15

91.04

3.62

2/66

1/2090

5/218

11/211

6/238

83/69.79

30/7

12

1878

27.03

95.89

3.52

2/41

1/342

0/0

11/358

3/63

58/48.18

38/2

Total

24,716

367.14

23/4255

11/5801

38/1503

93/1877

39/1540

744/632.39

454/48

Ave.

96.07

3.51

*Ch. = Chromosome, Ave. = Average; frag. = fragment; Centr. = centromeric; ^a The predicted chromosome size based on optical map was used as the total mass to compute the percentage of the matching fragment mass. Gap or misassembly masses in the alignments were calculated based on the optical mapping data.

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