Table 1 Summary statistics of differential SNPs and their corresponding genes identified by RAD sequencing
Data filtering criteria | Total No. | TSC | TY | TSY | TSC and TY | TSC and TSY | TY and TSY | TSC, TY and TSY |
|---|---|---|---|---|---|---|---|---|
1. Total No. of SNPs | nd | 579,352 | 601,837 | 598,703 | nd | nd | nd | nd |
2. No. of SNPs with differential allele frequency (FDR < 0.05) | nd | 58,850 | 46,542 | 20,402 | nd | nd | nd | nd |
3. No. of SNPs with differential allele frequency in annotated genes (FDR < 0.05) | 25,501 | 10,986 | 5660 | 2207 | 3005 | 665 | 2330 | 648 |
4. No. of annotated genes with differential SNPs (FDR < 0.05) | 6664 | 1456 | 654 | 218 | 1575 | 430 | 532 | 1799 |
5. No. of SNPs with differential allele frequency in annotated genes causing amino acid changes (FDR < 0.05) | 4668 | 1993 | 1043 | 403 | 537 | 135 | 433 | 124 |
6. No. of annotated genes with differential SNPs causing amino acid changes (FDR < 0.05) | 2308 | 378 | 146 | 43 | 622 | 162 | 168 | 789 |
7. No. of SNPs with differential allele frequency in annotated genes causing amino acid changes (FDR < 0.0001) | 582 | 310 | 148 | 58 | 40 | 1 | 23 | 2 |
8. No. of annotated genes with at least one differential SNP with FDR < 0.001 | 3144 | 431 | 81 | 13 | 842 | 194 | 257 | 1326 |