Fig. 4

Bcftools reported zero read depth for the deletion region in the reference genome, leading to the underrepresentation of the major variant (the deletion). This absence of the major variant subsequently enables the occurrence of FP point mutations (minor variants) by meeting the variant frequency threshold. a Sequence alignment reveals a deletion in 92 reads (partially displayed) in reference positions 193–217 bp when aligned to the reference genome. b Illustration of an example where bcftools reported zero read depth of this deletion (the major variant) in 92 reads. A “.” represents that the read depth of the deletion region was not reported. A “-” represents that the read depth of the deletion region was correctly reported. c,d The impact of the QUAL criterion on the accuracy of point mutation identification by bcftools. The QUAL reported by bcftools indicates the Phred-scaled quality score for a variant, reflecting the confidence in the existence of the variant at that position. The blue line represents the QUAL threshold for bcftools selected in this study. QuickVariants neither compute QUAL nor utilize QUAL for variant filtering. c Effect of the QUAL criterion on the accuracy of point mutation identification by bcftools in sample BaOv with a 1e-06 mutational density. d Effect of the QUAL criterion on the accuracy of point mutation identification by bcftools in sample AkMu with a 4e-2 mutational density