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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         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
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