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Table 3 Validation of SNP calling

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

  

On target regions of RRL

  

SNP

Not SNP

SNP dataset generated by WGS

SNP

222,028

77,136

 

Not SNP

35,603

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  1. SNP calling results generated by RRL sequencing and WGS were compared by calculating the number of loci identified as SNPs by two methods equally or differently regardless of the concordance of genotyping. From the results the false discovery rate of RRL method was about 13.82% (35,603/(222,028+35,603)) and false negative rate was 25.78% (77,136/(77,136+222,028)).
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BMC Genomics

ISSN: 1471-2164

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