For genotyping, reads from the segregants along with both SK1 and S96 (a haploid strain isogenic to S288c) parental strains were aligned to the S288c reference genome (build R63) using Novoalign (v2.07.06; http://www.novocraft.com/), allowing for unique alignments.
In order to maximize the sensitivity of presence/absence genotyping, reads from all samples (for example, AA, AB, H, and D) were combined before clustering, and after clustering the number of reads from each sample were counted to determine patterns of SV sharing among the samples.
About 39% (139) of this set can be accounted for by differences in the sequence coverage between the shotgun reads and the resequencing genotyping reads (Table 2), whereas the remaining part of this set is strongly biased towards SNPs that are not polymorphic between BN and wild rat 1 and thus could not have been discovered in the shotgun experiment.
Consequently, the number of variant reads observed (X) at a position depends on the true genotype, read depth and nucleotide-read error.
Average aortic root diameter was calculated, and a third independent reader, also blinded to animal genotype, read any image for which the difference between readers 1 and 2 fell outside of 1 SD of the average difference between readers 1 and 2. When a third read was obtained, all three measurements were averaged to determine the aortic root diameter.
The raw genotype reads were subject to quality control, and the SNPs were positioned with reference to the mm9/build37 assembly.
Due to the polyploid nature of these plants and a potential high level of intra-organism and inter-organism variation, such as genome rearrangements or paralogue genes unique to one genotype, we decided to not combine genotype reads.
The laboratory technician who performed the genotyping and read the genotype data was blinded to the patients' clinical data.
Also, when genotypes are read, heterozygote genotypes could, theoretically, be more ambiguous, and therefore more likely to be scored as "missing," than homozygote genotypes.
Second, incomplete digestion of PCR product (relevant only when using the RFLP technique, not the TaqMan technique) or poor amplification of one of the alleles will lead to heterozygous genotypes being read as homozygous genotypes [ 53].
