TABLE 3.

Mutation rates for Mut2, Mut3, and Mut4 lines grown in bottlenecks for 160 generations

Base substitution mutations
Strain	No. mutations	% genome ≥7× coverage	Genome Size (bp) adjusted	Mutation rate (per base per gen ×10−9)
Mut2	6	41	9,898,136	3.8
Mut3	9	69	16,657,838	3.4
Mut4	13	84	20,279,107	4.0
Average				3.7
Single-nucleotide indel mutations in 5- to 13-nt HP tracts
Strain	No. mutations	No. HP tracts >7× coverage		Mutation rate (per HP tract/generation × 10−7)
Mut2	6	57,502		6.5
Mut3	15	99,714		9.4
Mut4	27	122,816		14
Average				10
Single-nucleotide indel mutations in 8- to 13-nt HP tracts
Strain	No. mutations	No. HP tracts >7× coverage		Mutation rate (per HP tract/generation × 10−7)
Mut2	4	2,820		89
Mut3	10	7,054		89
Mut4	19	8,696		140
Average				110

The base substitution mutation rate was determined by calculating the percentage of the genome in which at least sevenfold DNA sequencing coverage to unique regions was obtained. This was done because our statistical analysis did not have sufficient power to reliably detect heterozygous mutations in regions with lower coverage. This information was used to calculate the mutation rate on the basis of the following formula: (number of mutations)/(160 generations)/(adjusted genome size), with the diploid S. cerevisiae genome size determined as 24,141,794 bp (http://www.yeastgenome.org/). To obtain indel mutation rates, we first determined the number of HP tracts of a given length in unique regions of the genome which had ≥ sevenfold sequence coverage. We then used the following equation to calculate mutation rate: (number of indels)/(160 generations)/(number of HP tracts with ≥ sevenfold coverage).