Table 4

Scores for Arabidopsis assemblies determined using the pooled BAC and WGS strategies

Size (Mbp)

Method

Match

Relocation

Inversion

Redundancy

Coverage

Scaffold N50

Number of scaffolds


chr1

30.4

WGS

0.501

0.986

0.957

0.891

90.42%

chr2

19.7

WGS

0.496

0.940

0.954

0.846

84.97%

chr3

23.5

WGS

0.503

0.988

0.939

0.893

90.09%

207,281

3,268

chr4

18.6

WGS

0.479

0.992

0.950

0.778

76.01%

chr5

30.0

WGS

0.492

0.993

0.955

0.804

83.02%


chr1

30.4

Pooled

0.512

1.000

0.968

0.979

94.11%

369,269

497

chr2

19.7

Pooled

0.518

0.998

0.962

0.982

96.01%

534,038

291

chr3

23.5

Pooled

0.515

0.998

0.953

0.978

97.23%

464,102

431

chr4

18.6

Pooled

0.518

0.999

0.955

0.977

93.43%

355,538

370

chr5

30.0

Pooled

0.537

1.000

0.967

0.978

96.36%

750,202

390


Assembly evaluation scores and scaffold statistics are shown for the Arabidopsis chromosome pseudomolecules obtained from assembling WGS and pooled BAC data. Chromosome scaffold statistics for pooled assemblies are averages over the values for each pool in that chromosome. Optimized assembly parameters were used.

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

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