Skip to main content
Fig. 3 | BMC Bioinformatics

Fig. 3

From: An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome

Fig. 3

Tools and variables used in the experiment. Paired-end datasets of differing read lengths (50–1,000 bp) were mapped using Bowtie2 and BWA-SW with either high (2 % mismatches) or low (14 % mismatches) mapping stringency. The de novo assemblies computed with Velvet and Allpaths-LG were used as references, as well as the original A. thaliana reference sequence (control). All the resulting mappings underwent SNP calling with the variant callers FreeBayes and GATK, with and without filtering for read mapping quality. The resulting SNPs were filtered by coverage depth (< 150) and these call sets were compared to their unfiltered counterparts. For the final SNP counts, only biallelic entries with a SNP quality score greater than 20 were used

Back to article page