Table 1 Variant alleles found in 30 control strains (top), 23 neutrally transformed strains (middle), and six gene deletion strains (bottom)
30 Nontransformed
ChrPosReferenceAlternateACStrainAOROMF (%)GeneEffect
4574814TAATAAA1WT5439505155aPromoter
23 Neutrally Transformed
ChrPosReferenceAlternateACStrainAOROMF (%)GeneEffect
222453G(T)11CG(T)12C1G418_2010010006794bIntron
2303154TG1NAT_40290100STE6cSilent
3422414CT1NAT_6480100LIV10dE508K
1479613GC2G418_2836099CAT2ePromoter
G418_47
Six Gene Deletion Strains
ChrPosReferenceAlternateACStrainAOROMF (%)GeneEffect
11524172AC1pkr1∆49010000593fSilent
12183532GT1yrm103∆24010000823gSilent
21492740AG1ssn801∆25010004048hV471A
5410958G(A)10TG(A)9T1pkr1∆3319701397i3′ UTR
691956AG1ssn801∆2819702524jSilent
61082445CT1yrm103∆4129502146kT236I
71162733GA1ssn801∆21010005900lS29L
8531945GC1ccd6∆56010003269mP58R
91050856GC1yrm103∆310100VPS4nP110A
14837564AG(TCG)4AG(TCG)51ssn801∆13010005636o5′ UTR
11231133TCAGAG6All 6509807362pE68S
71278590ATTATTT6All 627291N/AIntergenic
  • Chr, chromosome on which the variant occurs; Pos, coordinate of the variant in the KN99α reference genome sequence; Reference, reference allele; Alternate, alternate allele; AC, “alternate count,” the number of strains with the alternate allele; Strain, the strain or strains in which the alternate allele is found; AO, “alternate observations,” the mean number of reads supporting the alternate allele in strains with the alternate allele; RO, “reference observations,” the mean number of reads supporting the reference allele in strains with the alternate allele; MF, “mean fraction,” the mean fraction of reads supporting the alternate allele in strains with the alternate allele; Gene, the name or KN99 gene identifier (CKF44 number) of the gene affected by the variants; Effect, the effect of the variant on the protein encoded by the indicated gene or location in the indicated gene.

  • a Protein-tyrosine-phosphatase.

  • b Hypothetical protein.

  • c Pheromone transporter.

  • d Homolog of S. cerevisiae gene RPP1.

  • e Catalase.

  • f Homolog of S. cerevisiae gene AIM18

  • g Cadmium ion transporter.

  • h Brg1-associated factor b.

  • i Mitochondrial membrane transport.

  • j Homolog of S. cerevisiae gene YKL111C.

  • k Homolog of S. cerevisiae gene ALE1.

  • l Glycine-tRNA ligase.

  • m Aldehyde dehydrogenase.

  • n ATPase.

  • o Homolog of S. cerevisiae gene TIF4632.

  • p Single-stranded DNA binding protein.