Table 4. Genome-wide nucleotide variation in evolved clonal isolates.
| Population | Clone ID | SNPs | Intergenic | Genic | Synonymous | Missense | Nonsense | Alleles (% in final population±95% CI) |
| G1 | G1c1 | 9 | 1 | 8 | 2 | 6 | 0 | CCR4 E724V (29±3) |
| PTH2 I138M (26.5±0.3) | ||||||||
| GIN4 L1079M (22±6) | ||||||||
| BRR2 G524S (28±1) | ||||||||
| MMS2 F77S (23±4) | ||||||||
| SAP185 synonymous (39±5) | ||||||||
| CST9 synonymous | ||||||||
| YNR071C S177L | ||||||||
| Intergenic between SPP2 and SMP3 | ||||||||
| G1 | G1c2 | 1 | 1 | 0 | 0 | 0 | 0 | SNF6 LTR insertion (1.7) |
| Intergenic between AGC1 and YPR022C | ||||||||
| G2 | G2c2 | 4 | 0 | 4 | 0 | 3 | 1 | TFC3 G877K |
| SIM1 A317V | ||||||||
| WHI2 Q228X | ||||||||
| YMR185W A926V | ||||||||
| MTH1 retrotransposon insertion | ||||||||
| G4 | G4c1 | 3 | 0 | 3 | 0 | 2 | 1 | GSH1 D188F (100) |
| BNI5 R367I | ||||||||
| RIM15 S1580X | ||||||||
| P1 | P1c2 | 2 | 0 | 2 | 0 | 2 | 0 | SIR1 C135Y (56±8) |
| CKA2 D186N (60±11) | ||||||||
| P2 | P2c2 | 1 | 0 | 1 | 1 | 0 | 0 | KGD1 synonymous |
| P3 | P3c2 | 3 | 1 | 2 | 0 | 2 | 0 | SLH1 E193K (100±8) |
| URB2 E1018D | ||||||||
| Intergenic between YGL258W-A and YGL258W | ||||||||
| S1 | S1c1 | 3 | 0 | 3 | 2 | 0 | 1 | SGF73 E277X (22±1) |
| ERG1 synonymous (20±2) | ||||||||
| SFP1 synonymous | ||||||||
| S2S2 | S2c1S2c1 | 3 | 0 | 3 | 0 | 1 | 2 | SGF73 E294X (15±2) |
| UPF3 G6W | ||||||||
| PBP2 Y127X | ||||||||
| S4S4 | S4c1 | 3 | 2 | 1 | 0 | 1 | 0 | YEL007W Y81D |
| Intergenic between AGP1 and YCL023C | ||||||||
| Intergenic between YCR006C and tP(AGG)C | ||||||||
| Total | 32 | 5 | 27 | 5 | 17 | 5 |
We predicted the presence of SNPs using the SNPScanner algorithm on tiling microarray data. In order to confirm the prediction and identify the sequence change we sequenced the locus using PCR and Sanger sequencing.