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Table 3 Variation accuracy estimation by comparison with GIAB

From: A new massively parallel nanoball sequencing platform for whole exome research

  detected variants GIAB-specific variations Sensitivity (%) Precision (%)a F-measure (%)b
total in GIAB not in GIAB
SNV Hiseq-1 35,051 34,851 200 359 98.98 99.43 99.20
  Hiseq-2 35,026 34,793 233 417 98.82 99.33 99.07
  Hiseq-3 35,030 34,821 209 389 98.90 99.40 99.15
  Hiseq-4 35,037 34,842 195 368 98.95 99.44 99.20
  BGISEQ-1 35,073 34,883 190 327 99.07 99.46 99.26
  BGISEQ-2 35,069 34,876 193 334 99.05 99.45 99.25
  BGISEQ-3 35,071 34,886 185 324 99.08 99.47 99.28
  BGISEQ-4 35,048 34,881 167 329 99.07 99.52 99.29
  Hiseq-1 PE100 35,110 34,905 205 305 99.13 99.42 99.27
  Hiseq-2 PE100 35,056 34,855 201 355 98.99 99.43 99.21
  Hiseq-3 PE100 35,174 34,880 294 330 99.06 99.16 99.11
  Hiseq-4 PE100 35,143 34,897 246 313 99.11 99.30 99.21
indel Hiseq-1 2501 2453 48 197 92.57 98.08 95.24
  Hiseq-2 2493 2454 39 196 92.60 98.44 95.43
  Hiseq-3 2507 2457 50 193 92.72 98.01 95.29
  Hiseq-4 2508 2453 55 197 92.57 97.81 95.11
  BGISEQ-1 2542 2480 62 170 93.58 97.56 95.53
  BGISEQ-2 2571 2498 73 152 94.26 97.16 95.69
  BGISEQ-3 2553 2478 75 172 93.51 97.06 95.25
  BGISEQ-4 2564 2488 76 162 93.89 97.04 95.44
  Hiseq-1 PE100 2538 2498 40 152 94.26 98.42 96.30
  Hiseq-2 PE100 2512 2471 41 179 93.25 98.37 95.74
  Hiseq-3 PE100 2541 2474 67 176 93.36 97.36 95.32
  Hiseq-4 PE100 2523 2484 39 166 93.74 98.45 96.04
  1. aPrecision = true positive/(true positive + false positive). Precision instead of specificity was used because true negative dominate the region thus specificity is very close to 1
  2. bF-measure is the harmonic average of the sensitivity and precision. It combines sensitivity and precision in a single measurement