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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 %)