Fig. 3

Alignment and variant calling using a wild reference S. pennellii genome. a Alignment percentage of five different aligner settings: SOAP2, SOAP2-tuned, Bowtie2, Bowtie2-tuned and BWA-MEM calculated for domesticated tomatoes and wild relatives using the S. pennellii reference genome. The width of violin plot is proportional to the density of the data, and boxplot is plotted inside violin plot showing quantiles and outliers. b Mapping percentage of samples for different aligner setting. The mapping percentages are relative to the IBS distance to the reference genome. c SNP identification of four tomato samples was performed in chromosome 1 in S. pennellii reference genome. The corresponding physical positions of SNPs in the S. lycopersicum reference were plotted. The grey dots represented the SNPs that were able to be located at the corresponding positions in S. lycopersicum genome, red dots represented the SNPs that were unable to be located to corresponding positions in S. lycopersicum genome. The percentage of corresponding SNPs were written next to the species name