Table 1

BAC-end sequence (BES) characteristics

Annotation

Retro-element

(RE)

Genes

(G)

G + RE

Transposable

elements (TE)

G + TE

Non-annotated

(NA)

Totals


Total ends

17928

17255

2,566

327

148

44,157

82,381

Total unique clustersa

7,401

11,233

913

201

44

32,147

51,939

Average cluster depth

2.42

1.54

2.81

1.63

3.36

1.37

1.69

Total unique sequenceb

58,25,082

81,60,879

7,59,831

1,54,620

44,218

2,02,54,481

3,51,99,111

Total clusters with SSRs

302

1,083

13

11

0

3,188

4,597

Total SSRs

593

1,483

21

15

0

4100

6,212

SSRs/100 Kbp

10.2

18.2

2.8

9.7

0

20

17.7

Selected SSR-BESsd

124

646

4

2

0

1943

2,719

Polymorphic SSRsc

32

241

0

0

0

568

839

Average number of alleles

5.0 ± 1.7

5.4 ± 1.7

na

na

na

5.8 ± 2.1

5.7 ± 2.0

Average PIC value

0.53 ± 0.20

0.58 ± 0.18

na

na

na

0.57 ± .19

0.57 ± 0.18


aTotal unique clusters represent the total number of sequence clusters plus the number of singleton (non-clustered) sequences.

bTotal unique sequence represents the sum of the nucleotide length of all unique sequence clusters.

cThree polymorphic markers are from BAC ends annotated as "chloroplast" and are not listed in this table.

d2,964 SSR markers were derived from 2,719 BESs, with some BESs containing multiple SSRs

Bohra et al. BMC Plant Biology 2011 11:56   doi:10.1186/1471-2229-11-56

Open Data