Table 3. Properties of the three causative sites identified by BSA-seq and confirmed by single site mutagenesis.

Mutant	Mutation Position		Mutation Type			Phenotypic Effect			Sequencing Depthd		Mutation Frequency
	Chr.	Position	Gene	DNA	Protein	Meana	Std Devb	Sel Coefc	Low Bulk	High Bulk	Low Bulk	High Bulk
YPW89	IV	1347028	SSN2	C→T	Q971Stop	+10.16%	−6.66%	0.140	121	83	0	0.22
YPW94	III	260366	TUP1	G→A	G696D	+6.93%	−14.39%	0.045	152	73	0	0.55
YPW102	XVI	679727	ROX1	G→A	R12K	−4.05%	−8.89%	0.015	102	77	0.96	0.30

BSA-seq, bulk segregant analysis coupled with high-throughput sequencing; Chr., chromosome.

^aMean expression of single site mutant relative to wild type expressed as a percentage of change in fluorescence phenotype relative to wild type.

^bStandard deviation of expression phenotype of the single site mutant strain relative to the reference strain.

^cSelection coefficient was measured by using competitive growth of each single site mutant against the control population, as described in the Materials and Methods.

^dNumber of sequencing reads overlapping the variable site in each bulk.