Table 2 Number of unfiltered variants in the real data set called by the individual variant callers
Variant found by variant caller | SNPs | Indels | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
BWA | Bowtie 2 | BWA | Bowtie 2 | ||||||||
HC | UG | FreeBayes | SAMtools | # of variants | % of all | # of variants | % of all | # of variants | % of all | # of variants | % of all |
+ | + | + | + | 48297 | 88.81 % | 43659 | 84.27 % | 2918 | 46.73 % | 2958 | 49.58 % |
+ | + | + | 440 | 0.81 % | 297 | 0.57 % | 532 | 8.52 % | 544 | 9.12 % | |
+ | + | + | 432 | 0.79 % | 273 | 0.53 % | 76 | 1.22 % | 77 | 1.29 % | |
+ | + | + | 296 | 0.54 % | 215 | 0.42 % | 638 | 10.22 % | 466 | 7.81 % | |
+ | + | + | 1332 | 2.45 % | 1078 | 2.08 % | 53 | 0.85 % | 66 | 1.11 % | |
+ | + | 222 | 0.41 % | 115 | 0.22 % | 18 | 0.29 % | 24 | 0.40 % | ||
+ | + | 82 | 0.15 % | 45 | 0.09 % | 254 | 4.07 % | 186 | 3.12 % | ||
+ | + | 57 | 0.10 % | 36 | 0.07 % | 235 | 3.76 % | 130 | 2.18 % | ||
+ | + | 367 | 0.67 % | 403 | 0.78 % | 56 | 0.90 % | 99 | 1.66 % | ||
+ | + | 164 | 0.30 % | 90 | 0.17 % | 23 | 0.37 % | 41 | 0.69 % | ||
+ | + | 798 | 1.47 % | 1021 | 1.97 % | 108 | 1.73 % | 156 | 2.61 % | ||
+ | 499 | 0.92 % | 178 | 0.34 % | 578 | 9.26 % | 342 | 5.73 % | |||
+ | 329 | 0.60 % | 330 | 0.64 % | 11 | 0.18 % | 40 | 0.67 % | |||
+ | 781 | 1.44 % | 3596 | 6.94 % | 256 | 4.10 % | 371 | 6.22 % | |||
+ | 285 | 0.52 % | 471 | 0.91 % | 489 | 7.83 % | 466 | 7.81 % | |||