Fig. 3.

Comparison of muver calls with previous Saccharomyces cerevisiae mutation accumulation experiments. a Log-transformed substitution (square) and indel (circle) mutation rates, per base pair per generation, determined across the genome by muver of by acquisition of resistance to 5-fluoroorotic acid (5-FOA) upon mutation of the URA3 reporter gene [63]. Solid lines are linear regressions for the log-transformed rates (R² = 0.988 and 0.908 for substitutions and single-base indels, blue and green, respectively; excluding pol1-L868 M msh2Δ substitutions in yellow; R² = 0.758 for multi-base indel rates in red). b Mutation counts from muver (purple) and pipe2015 (red; [18]) for MSH2-deficient S. cerevisiae presented here. Counts for mutations called by both pipelines are shown in green. c Fold-change in mutation counts (muver over pipe2015) in repeat tracts of 1-5 bp (purple), 6-10 bp (orange), 11-15 bp (grey) and more than 15 bp (gold). In calculating fold changes, pseudocounts were added to the numerator and denominator for categories where the pipe2015 totals were zero. Abbreviations: del. = deletions; ins. = insertions; dinuc. = dinucleotide repeats; trinuc. = trinucleotide or triplet repeats