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Table 3 Statistics of contigs and alignment

From: Analysis of microbial sequences in plasma cell-free DNA for early-onset breast cancer patients and healthy females

 

BBC

EJC

BC0145

BC0190

CGBC025

hg19-unmapped PE reads

19,995,200

12,453,737

29,541,269

17,104,576

28,010,855

Bacteria

Mapped PE reads (%)

15,504 (0.08%)

31,653 (0.25%)

1,432,423 (4.85%)

50,310 (0.29%)

45,858 (0.16%)

Fungi

Mapped PE reads (%)

451 (0.00%)

456 (0.00%)

590 (0.00%)

1,153 (0.01%)

996 (0.00%)

Viruses/Phages

Mapped PE reads (%)

1,367 (0.01%)

677 (0.01%)

1,528 (0.01%)

26,749 (0.16%)

1,267 (0.00%)

Bacteria

#Contigs

894

1,495

7,971

2,609

2,588

Max contig length

900

2,287

16,248

2,035

3,911

Min contig length

64

64

64

64

64

Median contig length

211

227

231

214

220

N50

215

266

1,616

219

237

#contigs w/ size ≥250 bp (%)

80 (9.0%)

558 (37.3%)

3,602 (45.2%)

333 (12.8%)

748 (28.9%)

#aligned contigs (also see Table 4)

54

381

2,456

225

451

Fungi

#contigs

44

38

215

92

78

Max contig length

315

235

352

427

262

Min contig length

65

64

64

64

64

Median contig length

71

84

71

84

73.5

N50

99

192

78

192

127

#contigs w/ size ≥250 bp (%)

2 (4.6%)

0 (0.0%)

3 (1.4%)

3 (3.3%)

1 (1.3%)

#aligned contigs

2

0

0

2

1

Viruses/ phages

#Contigs

75

62

287

155

72

Max contig length

655

546

336

695

274

Min contig length

64

64

64

64

64

Median contig length

68

84

70

73

74

N50

194

210

85

189

126

#contigs w/ size ≥250 bp (%)

9 (12.0%)

7 (11.3%)

10 (3.5%)

13 (8.4%)

1 (1.4%)

#aligned contigs

7

5

2

10

0