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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