Fig. 1

Experimental scheme for the generation of C. elegans strains to estimate variant calling performance. A Schematic representation of genetic variants in the two C. elegans strains. Two strains, namely ALT1 and ALT2, were derived from a common telomerase mutant worm. When CB4856 genome was used as a reference, all variants detected in the ALT1 and ALT2 assemblies can be divided into the following three types: (1) founder variants introduced during the process of starting mutant worm generation (blue bars); (2) variants acquired by common DNA damage events (yellow bars); and (3) variants acquired by strain-specific DNA damage events (gray bars). The location of each variant does not reflect the real location. B Comparison of various types of real variants and variants that were identified by sequencing and/or variant calling errors. Identified variants can be categorized as follows: (1) full match: if the identified variant exactly matched the corresponding real variant; (2) partial match: if the identified variant partially matched the corresponding real variant; (3) missing: if the real variant existed in the genome but no corresponding variant was identified; and (4) mis-calling: no real variant existed at a certain locus but the locus contained an identified variant; TP, true positive; FP, false positive. C Types of variants used for estimating the variant calling performance of CLR and HiFi. Founder variants can be accurately identified by utilizing the high-quality N2 genome. The number of shared founder variants between ALT1 and ALT2 was used to measure the true-positive detection performance for HiFi and CLR (left). The two strains contained true-positive variants acquired through common and strain-specific DNA damage in addition to falsely detected miscalled variants. The ratio of common acquired variants and strain-specific acquired variants was utilized to measure the false-positive detection performance for HiFi and CLR (right)