Table 3 Number of SNPs during SNP array designation
From: Development and evaluation of the first high-throughput SNP array for common carp (Cyprinus carpio)
Category | Original | Stage 1 | Stage 2 | |||||
|---|---|---|---|---|---|---|---|---|
Repetitive nucleotides | GC content | Unique mapping | Adjacent SNPs | Pre-screen | Probe QC | Final | ||
Transcriptome sequencing | Â | Â | Â | Â | Â | Â | Â | 147,026 |
  Non-synonymous | 47,137 | 32,489 | 32,315 | 25,211 | 11,813 | 9,669 | 8,204 | 8,204 |
  3′UTR | 19,639 | 13,734 | 12,758 | 11,314 | 5,340 | 3,819 | 3,616 | 3,616 |
  5′UTR | 8,145 | 6,488 | 6,420 | 5,042 | 2,516 | 1,864 | 1,603 | 1,603 |
  Others | 670,325 | 629,039 | 586,832 | 475,850 | 220,137 | 155,437 | 140,879 | 133,603 |
  Genome re-sequencing |  |  |  |  |  |  |  | 102,974 |
  Strain-shared | 809,662 | 745,423 | 660,045 | 532,121 | 213,189 | 168,216 | 157,579 | 100,974 |
  Strain-specific | 13,811,200 | 12,004,400 | 10,008,670 | 7,401,099 | 3,266,265 | 39,810 | 35,831 | 2,000 |
Total | 15,366,108 | 13,431,573 | 11,307,040 | 8,450,637 | 3,719,260 | 378,815 | 347,712 | 250,000 |