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Table 2 First major higher-order interaction. L o g 10-transformed means for the 5-way interaction between assembly, mapper, read length, MAPQ, and mapping stringency

From: An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

   

Length

50

100

150

300

500

1000

Assembly

Mapper

Stringency

MAPQ

      

Allpaths

Bowtie2

Relaxed

0

3.743

3.736

3.807

4.084

3.863

3.975

Allpaths

BWA

Relaxed

0

3.692

3.752

3.823

3.906

3.922

3.947

Allpaths

Bowtie2

Strict

0

3.349

3.445

3.480

3.529

3.571

3.621

Allpaths

BWA

Strict

0

1.729

1.755

1.760

1.759

1.758

1.739

Control

Bowtie2

Relaxed

0

0.000

0.000

0.000

3.856

0.920

0.226

Control

BWA

Relaxed

0

1.547

1.112

0.736

0.254

0.000

0.369

Control

Bowtie2

Strict

0

0.000

0.000

0.000

0.953

0.000

0.000

Control

BWA

Strict

0

1.248

0.866

0.595

0.270

0.075

0.075

Velvet

Bowtie2

Relaxed

0

2.960

3.399

3.572

4.084

3.691

3.838

Velvet

BWA

Relaxed

0

2.972

3.313

3.491

3.628

3.720

3.799

Velvet

Bowtie2

Strict

0

3.091

3.504

3.582

3.618

3.638

3.658

Velvet

BWA

Strict

0

1.779

1.806

1.834

1.834

1.825

1.798

Allpaths

Bowtie2

Relaxed

20

3.615

3.589

3.668

3.917

3.716

3.857

Allpaths

BWA

Relaxed

20

3.594

3.695

3.775

3.880

3.882

3.914

Allpaths

Bowtie2

Strict

20

3.143

3.306

3.366

3.448

3.507

3.562

Allpaths

BWA

Strict

20

0.000

0.000

0.000

0.000

0.000

0.000

Control

Bowtie2

Relaxed

20

0.000

0.000

0.000

3.451

2.497

2.246

Control

BWA

Relaxed

20

0.000

0.000

0.000

0.000

0.000

0.000

Control

Bowtie2

Strict

20

0.000

0.000

0.000

0.648

0.000

0.000

Control

BWA

Strict

20

0.000

0.000

0.000

0.000

0.000

0.000

Velvet

Bowtie2

Relaxed

20

2.322

3.002

3.281

3.842

3.519

3.733

Velvet

BWA

Relaxed

20

2.438

3.018

3.300

3.492

3.637

3.748

Velvet

Bowtie2

Strict

20

2.682

3.292

3.429

3.486

3.536

3.590

Velvet

BWA

Strict

20

0.000

0.000

0.000

0.000

0.000

0.000

Sed = 0.02191

         
  1. Sed standard error of the difference