Alignments of O. edulis in silico sequences

For the in silico SNPs, we investigated O. edulis transcriptome sequence data from eight individuals from the natural range (Cahais et al. 2012, Gayral et al. 2011). For the present study, the 454 and Illumina reads were assembled using a multi-kmer strategy (kmers: 37, 41, 45, 49, 53, 57 and 61, assembled with Velvet version 1.1.03). Contigs longer than 100 bp from every assembly were then meta-assembled with TGICL (http://compbio.dfci.harvard.edu/tgi/software/). The Illumina reads were remapped on the contigs using BWA (0.5.9-r16) and a compressed alignment file was produced using SAMtools view (version 0.1.11). The alignment file was then used to call the SNPs with SAMtools pileup and varFilter (version 0.1.11). In this database, we looked for SNPs that represented different contigs, with a depth ranging from 20 to 500 at the position and no other SNPs in the surrounding 120 bp. The SNP quality score was initially set at 20 but finally, due to the high number of SNPs available, we only used SNPs with the highest score of 227.