Summary of all detected mutations in HAP-treated clones.

aSee Materials and Methods for details of mutation detection. For haploid clones, terms “homozygous” and “heterozygous” are arbitrary and included for simplicity.
bValues for number of mutations are divided by 112.00363 for haploid strains and 224.00726 for diploid strains. Results are rounded to two decimal points. Homozygous mutations in diploids are treated as two heterozygous mutations.
cMajority of homozygous SNVs in diploid clones are results of recombination events (see Table S6 for details). Among five homozygous SNVs found in In LAN211-1, three are grouped together on the distal end of the right arm of ChrV. Among six homozygous SNVs in LAN211-4, four are grouped together on the distal end of left arm of chrV. Among 25 homozygous SNVs in LAN211-10, 22 are found together on the distal end of right arm of chrIV. All 13 homozygous SNVs found in LAN211-NM1 are localized in the left arm of ChrVI. These patches of homozygous mutations found in different clones are not due to the chromosome arm loss, because the coverage of genome assembly for the regions of homozygosity in the corresponding clones is the same as the average coverage throughout the whole genome.