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Table 1 Validation of the four categories of SNP on the GenoPea 13.2 KSNP Illumina genotyping BeadChip

From: De novo construction of a “Gene-space” for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources

  SNP in exon with primer in exon SNP in exon with primer partially in intron SNP in intron with primer in intron SNP in intron with primer partially in exon
Total number of SNP 7265 762 2712 427
Detected polymorphism 6514 (89.5 %) 685 (90 %) 2442 (90 %) 380 (89 %)
Non-detected polymorphism 551 (7.8 %) 45 (5.9 %) 185 (6.8 %) 33 (7.7 %)
Technical error 200 (2.75 %) 32 (4.2 %) 85 (3.1 %) 14 (3.3 %)