Table 2.
# 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 |
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).