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Table 4 SNP calling results

From: Benchmarking short sequence mapping tools

Tools

Log-odds ratio

 

5

100

200

300

400

500

600

700

800

900

1000

1000000

Bowtie

89479

24337

5082

2231

1076

648

426

281

0

0

0

1171

Bowtie2

200914

62178

10018

4200

2052

1156

767

537

0

0

0

2035

BWA

192050

52115

9028

4049

1894

1087

737

525

0

0

0

2067

SOAP2

174475

49302

8552

3824

1837

1030

704

508

0

0

0

1941

Novoalign

69798

17586

4061

1875

936

519

363

252

0

0

0

941

GSNAP

207920

69015

11416

4928

2482

1325

971

617

0

0

0

2602

  1. SNP calling results when using the different tools. Each row represents a different tool while each column shows the number of SNPs detected with a log-odds ratio, which is a measure of the accuracy of the detected SNP, centered around the given values. The larger the log-odds ratio is, the more accurate the detected SNP becomes.