Table 4 Total number of SNPs before quality control (pre-QC), post quality control (post-QC) and the percentage of SNPs retained for each autosomal chromosome.
Chromosome | Total markers pre-QC | Total markers post-QC | %Markers post-QC |
|---|---|---|---|
1 | 5926 | 4054 | 9.55 |
2 | 4141 | 2546 | 6.00 |
3 | 3575 | 2600 | 6.13 |
4 | 3807 | 2626 | 6.19 |
5 | 3009 | 2103 | 4.95 |
6 | 4360 | 2870 | 6.76 |
7 | 3943 | 2823 | 6.66 |
8 | 3533 | 2376 | 5.60 |
9 | 3856 | 2730 | 6.43 |
10 | 2873 | 1967 | 4.63 |
11 | 2344 | 1623 | 3.82 |
12 | 2513 | 1526 | 3.59 |
13 | 4435 | 3088 | 7.28 |
14 | 4087 | 2556 | 6.02 |
15 | 3607 | 2534 | 5.97 |
16 | 2386 | 1748 | 4.12 |
17 | 2178 | 1350 | 3.18 |
18 | 1757 | 1311 | 3.09 |
