Table 4 Metrics of assemblies of the c22 dataset

Number of contigs

120712

231594

120462

113428

Genome size (bp)

34894545

34894545

34894545

34894545

Total contigs length

45667531

55880641

44737441

43099113

- as  % of genome

130.87

160.14

128.21

123.51

Mean contig size

378.32

241.29

371.38

379.97

Median contig size

132

101

120

117

Longest contig

41352

41352

41352

39379

Shortest contig

102

100

100

101

Contigs > 500 bp

13467 (11.16%)

13416 (5.79%)

13439 (11.16%)

13430 (11.84%)

Contigs > 1 Kbp

8700 (7.21%)

8684 (3.75%)

8696 (7.22%)

8578 (7.56%)

Contigs > 10 Kbp

264 (0.22%)

264 (0.11%)

264 (0.22%)

228 (0.20%)

N50

1614

815

1699

1617

L50

5684

10118

5416

5488

NG50

2737

2739

2733

2461

LG50

3120

3113

3121

3429

Plantagora metrics

RJ

SGA

Edena

LEAP

Covered Bases

34343945

34357693

34300114

12968118

Ambiguous Bases

159997

154584

182952

696334

Misassemblies

4

4

4

3693

Misassembled Contigs

4

4

4

2344

Misassembled Contig Bases

1283

417

1245

2797710

SNPs

104

125

120

46270

Insertions

5

2

1

2403

Deletions

43

23

28

5187

Positive Gaps

2679

2471

2925

26495

Internal Gaps

0

0

0

21

External Gaps

2679

2471

2925

26474

- total length

547408

558921

589979

19064103

- average length

204

226

202

720

Negative Gaps

110888

218908

110811

18198

Internal Overlaps

0

0

0

17

External Overlaps

110888

218908

110811

18181

- total length

−10247647

−20078971

−9424823

−1859835

- average length

−92

−92

−85

−102

Redundant Contigs

864

1158

607

6329

Unaligned Contigs

3262

4686

3221

60563

- partial

18

57

21

3252

- total length

462668

599320

447922

27666823

Ambiguous Contigs

2631

3876

2619

799

- total length

369284

483895

366418

93102