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Table S1 Yeast strains - Overview of 88 clinical and non-clinical Saccharomyces cerevisiae strains genotyped by hybridization of genomic DNA onto separate GeneChip® S. cerevisiae Tiling 1.0R Arrays (Affymetrix); ND, not determined; NA, not applicable. All strains have been deposited in, and should be requested from, the Phaff Yeast Culture Collection (http://www.phaffcollection.org/)

Table S2 Oligonucleotide primers used for polymerase chain reaction (PCR) amplification of the genetic loci covered by single feature polymorphisms (SFPs) 65,184, 65,185, 65,186 and 65,201 in S. cerevisiae strain YJM1199

Fig. S1 Distribution of single feature polymorphisms in the nuclear genome of Saccharomyces cerevisiae, identified based on the bimodal distribution of the hybridization intensity profiles of features with unique occurrences in the S. cerevisiae S288c reference genome that cover polymorphic loci and microarray hybridizations of genomic DNA of segregants of 88 S. cerevisiae isolates onto separate Affymetrix GeneChip® S. cerevisiae Tiling 1.0R Arrays; black, total number of microarray features per kbp; red, number of features covering polymorphic sites per kbp.

Fig. S2 Distributions of the frequency of the S288c-like allele class per microarray feature (a) and per strain (b), calculated based on the hybridization of genomic DNA of segregants of 88 clinical and non-clinical Saccharomyces cerevisiae isolates onto separate GeneChip® S. cerevisiae Tiling 1.0R Arrays (Affymetrix).

Fig. S3 Underlying DNA sequence polymorphisms of single feature polymorphisms (SFPs) found to be associated with clinical origin in Saccharomyces cerevisiae; triplet codons follow the S. cerevisiae S288c reading frame; polymorphic nucleotides and amino acids are indicated in bold; *, intergenic region; genome positions refer to the February 2011 assembly of the S. cerevisiae S288c reference genome.

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