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Table 2 Number of unfiltered variants in the real data set called by the individual variant callers

From: VariantMetaCaller: automated fusion of variant calling pipelines for quantitative, precision-based filtering

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 %