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Table 5 Comparison of RRL sequencing and Illumina Beadchip genotyping results

From: Comprehensive evaluation of SNP identification with the Restriction Enzyme-based Reduced Representation Library (RRL) method

      Tsp 45I RRL sequencing   
   Concordance    Discordance   
    HOM ref. HOM mut. HET ref. HET mut. Total
Illumina genotyping HOM ref. 55,435(99.95%) --- 5 22 0 27
  HOM mut. 19,847(99.80%) 21 1 18 0 40
  HET ref. 21,244(92.56%) 1458 245 3 2 1708
  HETmut. 0(0.00%) 4 0 0 0 4
  Total 96,445(98.19%) 1483 251 43 2 1779
  1. The alleles genotyped by Illumina platform and RRL sequencing were classified into four categories: HOM ref. (homozygotes where both alleles are identical to the reference), HOM mut. (homozygotes where both alleles differ from the reference), HET ref. (heterozygotes where only one allele is identical to the reference), and HET mut. (heterozygotes where both alleles differ from the reference and also differ from one another).