Table 1.
Number of mismatches in aligned reads.
Table 2.
Calling accuracy of SNPs from alignment data containing multiple samples.
Figure 1.
Improvement of SNP/indel calling accuracies of various DNA variant callers by Coval-Refine.
(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).
Figure 2.
Improvement by Coval-Refine of SNP/indel calling accuracy of variant calling tools for mouse alignment data.
(A) SNP calling accuracy with or without Coval-Refine. (B) Indel calling accuracy with or without Coval-Refine. A simulated mouse genome was aligned with real mouse read data using BWA. The alignments were filtered (+, striped bars) or not filtered (–, plain bars) with Coval-Refine. Homozygous SNPs and indels were called with the indicated variant callers under the same conditions as in Figure 1.
Figure 3.
Improvement of targeted alignment by Coval-Refine.
Rice whole-genome sequencing reads (63 million 75 bp paired-end reads) were aligned to chromosome 10 (A and B) or a 1 Mb region of chromosome 10 (C and D) of the simulated rice genome. Snapshot views of the alignments, corresponding to positions 1,338,000 to 1,342,538, with (B and D) or without (A and C) the Coval-Refine tool (basic mode) are represented. The shown alignment views were obtained with an IGV 1.5 viewer [46]. Shaded bars represent reads, and colored lines in bars non-reference bases. Blue arrowheads indicate true positive SNPs that had been introduced into the rice genome using the Coval-Simulate tool.
Figure 4.
Improvement of SNP/indel calling accuracy by Coval-Refine in targeted alignment.
The whole chromosomes (All chr), chromosome 10 (Chr10), a 1 Mb fragment of chromosome 10 (Chr10-1M: positions 1000001 to 2000000 of Chr10) from the simulated rice genome were aligned with 75-bp paired-end reads sequenced from the whole rice genome using BWA. The alignments were filtered (+, bars in dark- and middle-red and in dark- and middle-blue) or not filtered (–, bars in light red and in light blue) with Coval-Refine in the basic mode. Two different filtering conditions of Coval-Refine for mismatch reads were applied; one is the default option for removing reads with three or more mismatches (middle-red and middle-blue bars), the other removing the second paired-end mate read when the first mate is filtered and removing a read pair that contained more than two total mismatches (dark red and dark blue bars). The mean coverage of read depth before and after (indicated with parentheses) the Coval-Refine treatment is indicated under the reference chromosome name. Homozygous SNPs and indels were called as in Figure 1. TPR and FPR for the called SNPs are shown with red and blue bars, respectively.
Table 3.
Increased mismatches of reads observed in a targeted alignment.