Table 1.
Distribution of SNPs that passed quality control on the chicken genome
| Chromosome | No. SNPs | Physical length (Mb)c | Marker density (kb/SNP) | 5% chromosome-wide significance thresholdd |
|---|---|---|---|---|
| 0a | 5979 | – | – | 8.36E-06 |
| 1 | 81,335 | 195.3 | 2.40 | 6.15E-07 |
| 2 | 50,755 | 148.8 | 2.93 | 9.85E-07 |
| 3 | 45,028 | 110.4 | 2.45 | 1.11E-06 |
| 4 | 33,760 | 90.2 | 2.67 | 1.48E-06 |
| 5 | 24,678 | 59.6 | 2.41 | 2.03E-06 |
| 6 | 16,436 | 35.0 | 2.13 | 3.04E-06 |
| 7 | 17,826 | 36.2 | 2.03 | 2.80E-06 |
| 8 | 13,667 | 28.8 | 2.10 | 3.66E-06 |
| 9 | 14,291 | 23.4 | 1.64 | 3.50E-06 |
| 10 | 14,631 | 19.9 | 1.36 | 3.42E-06 |
| 11 | 10,749 | 19.4 | 1.80 | 4.65E-06 |
| 12 | 11,590 | 19.9 | 1.72 | 4.31E-06 |
| 13 | 8589 | 17.8 | 2.07 | 5.82E-06 |
| 14 | 10,062 | 15.2 | 1.51 | 4.97E-06 |
| 15 | 7697 | 12.7 | 1.64 | 6.50E-06 |
| 16 | 273 | 0.5 | 1.96 | 1.83E-04 |
| 17 | 7113 | 10.5 | 1.47 | 7.03E-06 |
| 18 | 7292 | 11.2 | 1.54 | 6.86E-06 |
| 19 | 6517 | 10.0 | 1.53 | 7.67E-06 |
| 20 | 7321 | 14.3 | 1.95 | 6.83E-06 |
| 21 | 6786 | 6.8 | 1.00 | 7.37E-06 |
| 22 | 2877 | 4.1 | 1.42 | 1.74E-05 |
| 23 | 4584 | 5.7 | 1.25 | 1.09E-05 |
| 24 | 5541 | 6.3 | 1.14 | 9.02E-06 |
| 25 | 1860 | 2.2 | 1.18 | 2.69E-05 |
| 26 | 4485 | 5.3 | 1.19 | 1.11E-05 |
| 27 | 3784 | 5.2 | 1.38 | 1.32E-05 |
| 28 | 3862 | 4.7 | 1.23 | 1.29E-05 |
| LGE22C19W28_E50C23b | 124 | 1.0 | 7.78 | 4.03E-04 |
| LGE64b | 47 | 0.8 | 17.02 | 1.06E-03 |
| Total | 429,539 | 921.2 | 2.46 | 1.16E-07 |
aThese SNPs are not mapped to any chromosome
bTwo linkage groups
cThe physical length of the chromosome was based on the genome build Gallus_gallus-4.0/galGal4 (Nov. 2011)
dBonferroni-corrected 5% chromosome-wise significance threshold = 0.05/number of SNPs after quality control