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Table 7 PCR validation of Ae. tauschi i SNPs

From: Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

Category Sequenced loci(a) Total SNPs Validated SNPs False positive SNPs False positive SNPs due to reference False positive SNPs due to mapped reads SNP validation rate %
Sequence category
Genes 130 187 157 30 5 25 84.0
Repeat junctions 52 67 59 8 4 4 88.0
Uncharacterized 43 48 39 9 5 4 81.3
Total 225 302 255 47 14 33 84.4
Sequencing platforms
AB SOLiD 181 246 217 29 11 18 88.2
Roche 454 19 35 25 10 2 8 71.4
Illumina Solexa 84 96 82 14 6 8 85.4
Total(b) 284 377 324 53 19 34 85.9
  1. (a) Only loci with PCR products and Sanger sequences in both Ae. tauschii accessions (AL8/78 and AS75) were included in the table. One primer pair for each locus was designed for PCR amplification. (b) Since some SNPs were identified by more than one sequencing platform, the total numbers of SNPs therefore exceed 302.
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