Table 2

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

IRGSP sequence pseudomolecule

Optical map


Ch.

# Match frag.

Total match frag. mass (Mb)

Percent (%) out of total massa

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

2605

42.22

96.70

3.30

2/12

1/707

5/69

6/42

3/57

87/66.38

43/4

2

2272

35.23

97.48

3.41

1/6

1/429

3/21

2/12

2/10

73/65.55

27/1

3

2312

36.75

99.40

3.37

2/37

1/438

4/496

7/75

4/239

74/63.74

45/4

4

2230

33.65

93.99

3.49

2/111

0/0

5/192

15/359

15/1036

63/51.45

36/5

5

1985

29.03

96.57

3.60

2/255

1/54

5/96

9/66

8/314

61/52.26

29/3

6

2114

30.84

96.56

3.34

2/175

1/810

2/12

3/17

1/36

80/68.71

40/5

7

1974

29.20

98.48

3.60

1/13

2/84

0/0

8/145

3/55

64/57.67

39/4

8

1999

28.00

98.59

3.37

2/16

1/24

0/0

6/104

1/39

59/53.10

30/0

9

1613

22.31

84.25

3.63

2/3503

1/320

3/51

3/16

1/55

59/52.24

42/5

10

1664

22.51

93.95

3.35

2/54

1/117

5/671

7/79

3/62

45/36.53

28/4

11

1892

27.29

88.26

3.60

2/67

1/2090

4/178

9/141

5/635

91/76.07

23/8

12

1844

26.70

94.71

3.41

2/40

1/338

0/0

9/327

7/438

59/46.55

44/2

Total

24,504

363.73

22/4289

12/5240

36/1786

84/1383

53/2974

815/690

426/46

Ave.

94.91

3.46


*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

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