Table 1. Number of SNPs on each chromosomes between before and after in quality control
Chromosome | Before QC | After QC | Removed No. SNP |
No. SNP | No. SNP |
1 | 3,133 | 2,567 | 566 |
2 | 2,553 | 2,037 | 516 |
3 | 2,279 | 1,905 | 374 |
4 | 2,357 | 1,901 | 456 |
5 | 2,050 | 1,611 | 439 |
6 | 2,373 | 1,980 | 393 |
7 | 2,141 | 1,725 | 416 |
8 | 2,181 | 1,786 | 395 |
9 | 1,899 | 1,541 | 358 |
10 | 1,977 | 1,618 | 359 |
11 | 2,058 | 1,666 | 392 |
12 | 1,599 | 1,280 | 319 |
13 | 1,666 | 1,370 | 296 |
14 | 1,687 | 1,386 | 301 |
15 | 1,583 | 1,255 | 328 |
16 | 1,542 | 1,222 | 320 |
17 | 1,442 | 1,189 | 253 |
18 | 1,249 | 1,001 | 248 |
19 | 1,274 | 1,047 | 227 |
20 | 1,408 | 1,144 | 264 |
21 | 1,313 | 1,048 | 265 |
22 | 1,194 | 957 | 237 |
23 | 976 | 817 | 159 |
24 | 1,209 | 990 | 219 |
25 | 905 | 747 | 158 |
26 | 1,012 | 810 | 202 |
27 | 895 | 727 | 168 |
28 | 889 | 730 | 159 |
29 | 966 | 796 | 170 |
30 | 1,044 | 80 | 964 |
Total | 48,854 | 38,933 | 9,921 |
SNP, single nucleotide polymorphism; QC, quality control.