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Table 3 Second major higher-order interaction. L o g 10-transformed means for the 5-way interaction between assembly, mapper, variant caller, MAPQ and read length

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 Variant caller MAPQ       
Allpaths Bowtie2 FreeBayes 0 3.75 3.81 3.84 4.00 3.90 3.95
Allpaths BWA FreeBayes 0 3.68 3.72 3.75 3.77 3.77 3.73
Allpaths Bowtie2 GATK 0 3.34 3.37 3.45 3.61 3.53 3.65
Allpaths BWA GATK 0 1.74 1.78 1.84 1.90 1.91 1.96
Control Bowtie2 FreeBayes 0 0.00 0.00 0.00 2.76 0.63 0.08
Control BWA FreeBayes 0 2.80 1.98 1.33 0.52 0.08 0.44
Control Bowtie2 GATK 0 0.00 0.00 0.00 2.05 0.29 0.15
Control BWA GATK 0 0.00 0.00 0.00 0.00 0.00 0.00
Velvet Bowtie2 FreeBayes 0 3.65 3.82 3.88 4.10 3.92 3.92
Velvet BWA FreeBayes 0 3.61 3.64 3.71 3.76 3.76 3.75
Velvet Bowtie2 GATK 0 2.40 3.08 3.27 3.60 3.41 3.57
Velvet BWA GATK 0 1.14 1.48 1.62 1.70 1.78 1.85
Allpaths Bowtie2 FreeBayes 20 3.26 3.34 3.42 3.61 3.57 3.68
Allpaths BWA FreeBayes 20 1.72 1.77 1.81 1.87 1.89 1.90
Allpaths Bowtie2 GATK 20 3.50 3.56 3.62 3.76 3.65 3.74
Allpaths BWA GATK 20 1.87 1.92 1.96 2.01 2.00 2.02
Control Bowtie2 FreeBayes 20 0.00 0.00 0.00 1.95 1.34 1.23
Control BWA FreeBayes 20 0.00 0.00 0.00 0.00 0.00 0.00
Control Bowtie2 GATK 20 0.00 0.00 0.00 2.15 1.16 1.02
Control BWA GATK 20 0.00 0.00 0.00 0.00 0.00 0.00
Velvet Bowtie2 FreeBayes 20 2.48 3.12 3.34 3.64 3.54 3.66
Velvet BWA FreeBayes 20 1.20 1.50 1.64 1.74 1.80 1.85
Velvet Bowtie2 GATK 20 2.52 3.17 3.37 3.69 3.52 3.67
Velvet BWA GATK 20 1.24 1.52 1.66 1.75 1.84 1.90
Sed = 0.02191