Calling accuracy of SNPs from alignment data containing multiple samples.

The experimentally obtained rice reads (60, 30, and 15 millions) were mixed with the simulated 75 bp paired-end reads (60, 90, and 105 millions) generated by dwgsim with the rice simulated genome as template, respectively, yielding 120 millions of reads. The read mixtures were aligned to the rice simulated genome, resulting in alignments with average read depth of 24×, and each read set (sample) in the read mixtures was discriminated from the other read set using the RG tag. The SNPs were called using Coval-Call with a maximum of 80 reads covering the called positions, a minimum allele frequency at the called position of 0.2 (for 50% homozygous sample), 0.1 (for 50% heterozygous and 25% homozygous samples), or 0.05 (for 25% heterozygous and 12.5% homozygous samples), a minimum of three reads (for 50% homozygous sample) or two reads (for the others) supporting the called allele.aPercentage of the experimentally obtained rice read sample in the read mixture.bHeterozygosity of the experimentally obtained rice read sample (Homo: 0% heterozygosity, Hetero: 50% heterozygosity).