<p>(A) SNP calling accuracy with or without Coval-Refine. (B) Indel calling accuracy with or without Coval-Refine. The simulated rice genome was aligned with reads of the real rice genome (experimental reads) using BWA. Alignment data were filtered (+, red striped and blue striped bars) or not filtered (–, light red and light blue bars) with the Coval-Refine component (Coval-Refine, error correction mode), and homozygous SNPs and indels were called using the indicated variant callers. The SNPs and indels extracted by all the callers were further filtered under the same conditions, as described in the text. True positive rate (TPR, the number of successfully called SNPs or indels divided with the number of SNPs or indels introduced into the simulated genome, followed by multiplying with 100) is shown with light red and red striped bars, and false positive rate (FPR, the number of wrongly called SNPs or indels divided with the number of the totally called SNPs or indels, followed by multiplying with 100) with light blue and blue striped bars. The GATK pileline was carried out with (GATK BQSR) or without (GATK) the base quality score recalibration. A variant quality score recalibration in the GATK pipeline was omitted because of its unsuitability for our data. Instead it was replaced by simple filtering: a minimum allele frequency of 0.8 and a minimum allelic read depth of 2 (see Materials and Methods for details).</p
