Additional file 11: of Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding

SNP calling results. The file in VCF format provides the list of SNVs (SNPs and INDELs) identified in S. incanum, S. aethiopicum, S. melongena and S. torvum transcriptomes by mapping against S. melongena genome. For each SNV are indicated their position in eggplant genome scaffold, the allele of reference (eggplant genome allele) and the alternative allele (the transcriptomes allele), the quality of the SNV, the filters applied and detailed information about SNP calling process for each SNV and the different kind of transcriptome ID combinations in order to filter the intraspecific and interspecific polymorphisms. The different filter applied for in silico selection were: CS60 (the SNV is closer than 60 nucleotides to another SNV), HV0.05 (the region has more than 5.0 SVNs per 100 bases), CL60 (the SNV is closer than 60 nucleotides to the reference edge), CEF (SNV is not a CAP detectable by the enzyme: cheap_ones), VKF (it is not an SNP). (7Z 38609Â kb)