Table 1 Number and percentage of genes and SNPs identifed in the reference set and finally incorporated in the 62 K Axiom SNP chip ‘CcSNPnks’ for Affymetrix platform.
Sr. no. | Gene category | No. of reference genes | Total gene length (bp) | No. of SNPs identified | SNP density per Kbp | Average gene size (bp) | No. of SNPs per gene | No. of genes in the chip | Percentage of genes in the chip | No. of SNPs in the chip | No. of SNPs per gene |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | SCP | 10,064 | 12,218,733 | 430,380 | 35.2 | 1214 | 42.8 | 4314 | 44.80 | 24,537 | 5.7 |
2 | CSCSP | 5899 | 18,726,973 | 130,439 | 6.9 | 3175 | 22.1 | 4328 | 44.95 | 27,291 | 6.3 |
3 | AGCP | 192 | 617,039 | 13,979 | 22.7 | 3214 | 72.8 | 156 | 1.62 | 1536 | 9.9 |
4 | DRDRP | 874 | 2,907,123 | 48,387 | 16.6 | 3326 | 55.4 | 746 | 7.75 | 8090 | 10.8 |
5 | MCP | 96 | 201,088 | 22,477 | 111.8 | 2095 | 234.1 | 85 | 0.88 | 599 | 7.1 |
Total | 17,125 | 34,670,956 | 645,662 | 18.6 | 2024 | 37.7 | 9629 | 100 | 62,053 | 6.4 |
