Table 1. Number of SNPs and minor allele frequencies of SNPs by chromosome in 515 Ningxiang pigs after data edits, each genotyped with either an Illumina Porcine SNP60 array or GeneSeek Genomic Profiler (GGP) Porcine 50K arraya,b.
| Set I (212 pigs); Illumina Porcine SNP60 | Set II (303 pigs); GGP Porcine 50K | ||||
|---|---|---|---|---|---|
| Chromosome | N | MAF (SD) | Chromosome | N | MAF (SD) |
| 1 | 5,927 | 0.118 (0.156) | 1 | 3,782 | 0.132 (0.155) |
| 2 | 4,140 | 0.122 (0.159) | 2 | 2,679 | 0.136 (0.155) |
| 3 | 3,574 | 0.113 (0.153) | 3 | 2,366 | 0.127 (0.153) |
| 4 | 3,803 | 0.118 (0.156) | 4 | 2,451 | 0.122 (0.155) |
| 5 | 3,009 | 0.108 (0.151) | 5 | 1,956 | 0.119 (0.153) |
| 6 | 4,357 | 0.128 (0.157) | 6 | 2,779 | 0.131 (0.153) |
| 7 | 3,942 | 0.127 (0.156) | 7 | 2,364 | 0.143 (0.157) |
| 8 | 3,532 | 0.126 (0.159) | 8 | 2,357 | 0.134 (0.158) |
| 9 | 3,852 | 0.119 (0.156) | 9 | 2,562 | 0.129 (0.154) |
| 10 | 2,873 | 0.119 (0.155) | 10 | 1,358 | 0.136 (0.157) |
| 11 | 2,344 | 0.125 (0.160) | 11 | 1,505 | 0.139 (0.162) |
| 12 | 2,511 | 0.128 (0.159) | 12 | 1110 | 0.140 (0.158) |
| 13 | 4,432 | 0.121 (0.157) | 13 | 2,839 | 0.130 (0.154) |
| 14 | 4,086 | 0.129 (0.159) | 14 | 2,672 | 0.141 (0.159) |
| 15 | 3,605 | 0.118 (0.155) | 15 | 2,336 | 0.125 (0.155) |
| 16 | 2,386 | 0.132 (0.159) | 16 | 1,484 | 0.133 (0.155) |
| 17 | 2,176 | 0.121 (0.154) | 17 | 1,178 | 0.140 (0.159) |
| 18 | 1,756 | 0.102 (0.150) | 18 | 1,040 | 0.113 (0.149) |
| X | 3,304 | 0.058 (0.124) | X | 2,455 | 0.070 (0.133) |
| Total | 65,609 | 0.117 (0.155) | Total | 41,273 | 0.128 (0.154) |
a N = Number of SNPs by chromosomes;
b MAF (SD) = Mean (Standard deviation) of minor allele frequencies of SNPs by chromosomes.