From: Adaptable probabilistic mapping of short reads using position specific scoring matrices
 |  | Unfiltered | MapQ filtered |  | ||
---|---|---|---|---|---|---|
 | Mapper | Sensitivity | PPV | Sensitivity | PPV | Time (s) |
 a) ART paired-end length 36 |  |  |  | |||
 | BWA-PSSM | 0.974 | 0.974 | 0.935 | 1.000 | 211.18 |
 | BWA | 0.973 | 0.973 | 0.911 | 1.000 | 238.95 |
 | BWA-MEM | 0.899 | 0.899 | 0.753 | 1.000 | 404.35 |
 | Bowtie | 0.483 | 0.927 | * | * | 1578.74 |
 | Bowtie2 | 0.971 | 0.971 | 0.929 | 0.999 | 137.88 |
 | GEM | 0.976 | 0.071 | * | * | 91.46 |
 b) ART paired-end length 50 |  |  |  | |||
 | BWA-PSSM | 0.965 | 0.967 | 0.928 | 0.999 | 242.98 |
 | BWA | 0.911 | 0.943 | 0.785 | 0.999 | 261.53 |
 | BWA-MEM | 0.902 | 0.908 | 0.655 | 1.000 | 118.35 |
 | Bowtie | 0.433 | 0.951 | * | * | 656.37 |
 | Bowtie2 | 0.939 | 0.952 | 0.736 | 1.000 | 109.78 |
 | GEM | 0.927 | 0.399 | * | * | 48.79 |
 c) ART paired-end length 76 |  |  |  | |||
 | BWA-PSSM | 0.958 | 0.978 | 0.943 | 0.999 | 155.57 |
 | BWA | 0.697 | 0.963 | 0.498 | 0.999 | 210.34 |
 | BWA-MEM | 0.939 | 0.943 | 0.815 | 1.000 | 102.00 |
 | Bowtie | 0.366 | 0.969 | * | * | 213.10 |
 | Bowtie2 | 0.920 | 0.948 | 0.726 | 1.000 | 81.17 |
 | GEM | 0.906 | 0.692 | * | * | 29.47 |
 d) ART paired-end length 100 |  |  |  | |||
 | BWA-PSSM | 0.962 | 0.983 | 0.949 | 0.999 | 147.38 |
 | BWA | 0.352 | 0.971 | 0.201 | 0.999 | 194.03 |
 | BWA-MEM | 0.955 | 0.956 | 0.854 | 1.000 | 102.86 |
 | Bowtie | 0.365 | 0.981 | * | * | 168.39 |
 | Bowtie2 | 0.930 | 0.957 | 0.517 | 1.000 | 74.23 |
 | GEM | 0.900 | 0.779 | * | * | 23.25 |