Sanger sequencing chromatogram files for the manuscript Improved Genotype Inference Reveals Cis- and Trans-Driven Variation in the Loss-of-Heterozygosity Rates in Yeast

We selected three genomic regions to verify the genotypes called by our method. Region 1 spans positions 956964–957730 (all positions are given with respect to S288c reference genome R64) on the right arm of Chr XII and contains three markers. Region 2 spanned positions 1030968–1031837 on the right arm of Chr XV and contained six markers. These “control” regions were selected due to their relatively high conversion rates but even homolog bias. Region 3 spans positions 103380–103869 on the left arm of Chr XII and encompasses five HCHB markers (Table S7). We selected nine evolved clones from our MA experiment, PCR amplified these three regions and Sanger sequenced them. For all clones, the PCR fragments at Regions 1 and 2 were of the expected lengths (766 and 869 bp, respectively) and genotypes inferred from Sanger sequencing matched those obtained from the short-read data. Counter to expectation, the PCR amplification of Region 3 produced two fragments in all nine clones. One (“short”) fragment was of the expected length of 489 bp. The other (“long”) fragment was 651 bp long. Sanger sequencing of both fragments after gel extraction revealed that the short fragment perfectly matched the reference genome sequence. The first 423 bp of the long fragment perfectly matched the reference sequence at positions 103380–103802, while its last 68 bp mapped onto positions 103802–103869 on Chr XII in the reference genome. The intervening sequence of the long fragment contained two copies of 162 bp homologous to the reference sequence starting at position 103642. Chromatograms showed that the marker positions were heterozygous in the long fragment but homozygous for the BY alleles in the shorter fragment.