Table 2.
Minor allele frequency of validated SNPs
| SNPs | DH lines | INRA SP | INRA SY* | NCCCWA | 3 pop.* |
|---|---|---|---|---|---|
|
Monomorphic |
352 |
390 |
367 |
351 |
346 |
|
Potentially duplicated |
262 |
272 |
268 |
266 |
262 |
|
True |
344 |
296 |
322 |
341 |
350 |
|
MAF < 0.05 |
27 |
7 |
11 |
22 |
21 |
|
0.05 > = MAF < 0.10 |
30 |
33 |
30 |
36 |
26 |
|
0.10 > = MAF < 0.20 |
58 |
55 |
51 |
73 |
74 |
|
0.20 > = MAF < 0.30 |
63 |
55 |
71 |
56 |
66 |
|
0.0 > = MAF < 0.40 |
85 |
68 |
77 |
67 |
66 |
|
0.40 > = MAF < 0.50 |
81 |
78 |
82 |
87 |
97 |
| Total count | 958 | 958 | 957 | 958 | 958 |
SNPs were clustered into different categories based on their observed MAF in rainbow trout DH individuals and in the three population samples analysed
* one snp was not considered for MAF calculation because of genotyping failure in all samples.