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

Table 7 PCR validation of Ae. tauschi i SNPs

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

(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.

ISSN: 1471-2164