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Table 1 General BAC information

From: Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

        

Ratioe of

   

BAC

Linkage group

Genbank accession

SNP IDb

Length (bp)

Phase

Gap

ORFsc

Averaged EST coverage

EST- based coverage

Overall gene homeologyf

Gene densityg

gmw2-133d1

F

AC158503

8001

117591

III

0

13

32.6

38.2

3 of 13

1/9.05

gmw1-93l19

M

AC166092

 

51037

III

0

5

62.4

50.5

3 of 5

1/10.2

gmw1-105h23

O

AC187294

30491

134287

III

0

18

82.0

76.4

18 of 18

1/7.46

gmw1-15k6

I

AC160454

26051

148858

III

0

22

77.0

71.1

18 of 22

1/6.77

gmw1-11j16

L

AC166091

 

69947

III

0

9

82.2

83.0

2 of 9

1/7.77

gmw1-45m6

a

AC166742

 

143028

III

0

7

53.6

53.0

1 of 7

1/20.4

gmw1-5g16

O

AC169184

 

115953

II

2

11

74.0

68.8

4 of 11

1/9.66

gmw1-103e11

I

AC166090

 

89397

III

0

12

78.6

81.3

4 of 12

1/7.45

gmw1-58k3

O

AC185959

 

177331

II

2

8

50.7

47.5

3 of 8

1/22.2

gmw1-57d24

D1a

AC170860

20113

162359

II

2

19

75.0

71.5

3 of 19

1/9.02

gmw1-27d20

D1b

AC173959

16079

227022

I

6

24

65.4

61.9

3 of 24

1/9.46

gmw1-74i13

C1

DQ336954

5981

173654

III

0

18

68.3

70.4

13 of 18

1/9.65

gmw1-52d3

C2

DQ336955

 

98675

III

0

10

59.2

62.1

9 of 10

1/9.87

gmw1-13o17

D1a

AC196857

 

89030

II

5

9

41.5

48.0

1 of 9

1/11.1

gmw1-8g7

a

AC196858

 

53292

III

0

4

32.6

30.7

1 of 4

1/13.3

UMb001-24d13

E

DQ347960

13567

111223

II

1

8

84.0

79.3

3 of 8

1/13.9

UMb001-5f5

A2

DQ347961

42937

65475

II

2

5

91.9

94.6

3 of 5

1/10.9

Average

   

119303

  

14

59.1

59.05

 

1/11.1

  1. a Unmappable; no polymorphic SSRs identified or any matches of CDS to SNP data
  2. b SNP Ids are taken directly from Choi et al. (2007). EST sequence from which SNP derived found in Methods and Materials.
  3. c Does not include ORFs that are alternatively spliced
  4. d An average across the BAC of the number of bp supported by an EST or cDNA divided by the total number of bp for each annotation
  5. e A ratio of the total number of bp on the BAC that are annotated divided by the total number of bases that have EST or cDNA support
  6. f Count is based upon the number of homeologs shared between BACs out of the total number of genes
  7. g Gene density is in 1 gene per × number of kilobases
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BMC Genomics

ISSN: 1471-2164

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