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Table 2 T1 thresholds

From: MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

  # Reads1 # Reads2 # Alleles T1Galan Negmult T1Galan Simul T1Simul VarAmplEff T1Res1 T1Res2
ID 1186 306 5 50 50 74 62 66
102 418 326 6 62 61 92 176 64
153 329 205 6 62 61 93 111 121
161 416 382 4 38 38 77 113 80
165 252 524 5 50 50 128 240 137
190 295 418 6 62 61 138 102 139
211 285 443 4 38 38 63 155 69
215 506 829 6 62 61 64 64 59
223 410 335 5 50 50 100 88 87
225 458 383 4 38 38 58 53 52
248 239 463 6 62 61 68 67 71
252 536 549 5 50 50 73 61 65
256 409 297 5 50 50 74 117 93
266 341 342 5 50 50 86 105 57
272 317 317 5 50 50 53 53 69
281 430 324 7 75 74 120 111 177
347 171 261 6 62 61 83 96 73
430 300 288 4 38 38 62 57 43
449 545 283 4 38 38 82 91 75
492 133 1043 2 15 15 16 18 15
493 232 221 5 50 50 65 114 88
4695 361 701 6 62 61 113 142 120
4787 71 78 3 27 27 56 42 50
5092 273 535 6 62 61 98 75 111
5116 202 378 6 62 61 69 63 77
C3659 254 496 4 38 38 55 50 45
GO3120 220 456 5 50 50 203 93 314
GO3131 346 618 8 87 85 124 87 98
GO3132 511 794 4 38 38 51 54 53
GO3133 281 453 7 75 74 124 78 94
GO3134 363 678 8 87 85 124 102 342
GO3382 492 776 8 87 85 153 150 257
GO3394 482 609 3 27 27 28 25 25
GO3899 322 506 7 75 74 81 87 95
GO3922 235 359 6 62 61 75 68 136
GO3957 440 654 9 100 97 120 101 104
  1. The threshold T1 defined as the minimum number of sequences per individual required for reliable genotyping was computed by Galan et al. [13] using a negative multinomial distribution (referred as T1Galan Negmult). We approximated the threshold by a much less computationally intensive simulation approach (T1Galan Simul). T1Galan Negmult und T1Galan Simul do not take differences in allele amplification efficiencies into account. We used a simulation approach to investigate the effect of variation in amplification efficiency between alleles on the minimum number of reads required to achieve a reliable genotyping (T1Simul VarAmplEff). Assuming that we oversampled each amplicon, we estimated what would have been the minimum number of reads that would have given us the same genotypes as obtained with our 454 data for the two amplicon replicates per individual by resampling (T1Res1, T1Res2).