Table 3

Pooled BAC assembly scores for five genomes

Species

Pool Size

Match

Relocation

Inversion

Redundancy

Coverage

Scaffold N50

Number of scaffolds


A. thaliana

3M

0.527

0.994

0.954

0.962

87.44%

117,128

57

A. thaliana

6M

0.518

0.997

0.976

0.969

86.55%

126,619

100

A. thaliana

9M

0.511

0.927

0.985

0.975

85.72%

121,006

144

A. thaliana

12M

0.510

0.999

0.981

0.982

87.36%

147,618

152

V. vinifera

3M

0.524

0.997

0.955

0.988

84.76%

114,280

60

V. vinifera

6M

0.511

0.997

0.974

0.972

80.60%

113,117

143

V. vinifera

9M

0.510

0.997

0.953

0.969

82.96%

116,543

173

V. vinifera

12M

0.507

0.994

0.941

0.973

82.48%

115,403

226

O. sativa

3M

0.535

0.996

0.966

0.989

88.45%

112,776

39

O. sativa

6M

0.519

0.983

0.895

0.983

87.10%

140,891

90

O. sativa

9M

0.508

0.961

0.902

0.977

84.91%

117,728

141

O. sativa

12M

0.507

0.958

0.869

0.979

84.72%

114,523

219

P. trichocarpa

3M

0.529

1.000

0.984

0.981

82.68%

134,082

65

P. trichocarpa

6M

0.513

1.000

0.980

0.992

82.31%

119,756

114

P. trichocarpa

9M

0.508

1.000

0.995

0.992

81.39%

124,798

182

P. trichocarpa

12M

0.506

1.000

0.979

0.989

80.99%

117,268

256

S. bicolor

3M

0.542

0.945

0.944

0.957

86.56%

148,894

37

S. bicolor

6M

0.520

0.889

0.939

0.955

86.03%

147,854

81

S. bicolor

9M

0.508

0.922

0.898

0.953

84.59%

112,136

213

S. bicolor

12M

0.504

0.905

0.859

0.953

83.57%

96,480

274

Z. mays

3M

0.506

0.872

0.734

0.835

76.38%

52,719

140

Z. mays

6M

0.503

0.857

0.679

0.832

79.31%

40,526

320

Z. mays

9M

0.502

0.847

0.687

0.820

80.33%

37,394

485

Z. mays

12M

0.501

0.855

0.674

0.815

82.39%

37,122

577


Evaluation scores and scaffold statistics for assemblies determined using 15x linear + 5x paired read coverage and pool sizes 3 Mbp, 6 Mbp, 9 Mbp, and 12 Mbp are shown for all of the genomes studied. Default assembly parameters were used.

Haiminen et al. BMC Genomics 2011 12:194   doi:10.1186/1471-2164-12-194

Open Data