Skip to main content

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).