Putative EST-SNPs were detected using the QualitySNP program.
Using the QualitySNP program, we identified 33,433 high quality SNPs and 6,820 indels within 14,613 CAP3-assembled contigs (Fig 3).
SNP detection was performed with contigs of at least four sequences using the QualitySNP program (http://www.bioinformatics.nl/tools/snpweb/).nl/tools/snpweb/
We evaluated the structure of Coffea contigs to identify the percentage of coding sequences (CDS) in our dataset using the QualitySNP program tools [ 24].
SNPs were detected in silico and quality checked using the QualitySNP pipeline, as reported in Argout et al. and in ESTtik (http://esttik.cirad.fr).fr
CAP3 program was used to assembly sequences into 10 001 contigs and 55 961 singlets with an average size of 2.42 sequences per contig under default parameter, among which putative SNPs were detected in only 141 contigs using the QualitySNP program.
Haplotype-based SNPs were mined from ESTs of the 27 citrus cultivars and 3 groups (M12 – 12 mandarins, L7 – 7 limes/lemons, and C27 – all 27 combined) using the QualitySNP pipeline and summarized in detail (Additional file 1).
CAP3 program was used to assembly sequences into 20 934 contigs and 40 810 singlets with an average size of 4.005 sequences per contig under default parameter, among which putative SNPs were detected in 789 contigs using the QualitySNP program.
Using the QualitySNP programme, putative SNPs were identified in the assembled contigs that were covered by at least four reads and had at least two reads for each allele.
ESTs were searched for SNPs using the QualitySNP pipeline [ 8] in each of the 27 cultivars and in three cultivar groups, 12 mandarins (M12), 7 limes/lemons/citron (L7), and all 27 cultivars (C27).
Potential SNPs were detected using the QualitySNP program [ 36], which employs a haplotype-based strategy to detect reliable SNPs without requiring sequence traces, quality scores, or genomic sequence data.
