Fig. 1

Aligner performance comparison using real and simulated plant genomic datasets. a Alignment percentage of five different aligner settings: SOAP2, SOAP2-tuned, Bowtie2, Bowtie2-tuned and BWA-MEM calculated for domesticated tomatoes and wild relatives. The width of violin plot is proportional to the density of the data. Boxplots inside violin plot indicate quantiles and outliers. b Mapping percentage of each sample is shown relative to the IBS distance to the reference genome. c Alignment accuracy of five aligner settings using simulated dataset with varied number of SNPs per read and fixed 600 nt fragment size. Each axis represents the number of SNPs in the corresponding simulation. The blue color represents percentage of true positive (TP) alignments, pink color represents the percentage of false positive alignment (FP) and gold color represents the percentage of false negative (FN) alignments. d Alignment accuracy of five aligner settings using simulated dataset with varied size of INDELs per read and fixed 600 nt fragment size. Each axis represents the size of INDELs in the corresponding simulation. e Alignment accuracy of BWA-MEM on different crop species. Each axis represents different mutation rate which includes both SNP and INDEL mutations