Since molecular-based characterisation of microbes is becoming increasingly important, MOP-UP can aid microbiologists in finding the best loci on which to base such assays.
The distribution of best locus-specific P-values for each combined map is the null distribution of genome-wide adjusted P-values.
As the re-mapping of hippocampus weight QTLs in Fig. 2 shows, we see a significant QTL on Chr. 1, but we also see a non-significant indication of a QTL on Chr. 9. (best locus-wise P = 0.001).
Even in this study based on prior collected epidemiological measures, environmental factors can be found with effect sizes comparable to the best loci yet found by GWAS.
Our results based on the distribution of allelic frequencies highlight the importance of selecting the best loci for each analytical purpose.
Thus, by undertaking the pooled experiment, we would have identified 54% of the target loci (frequency difference 8%) and all 10 best loci, but at the cost of genotyping only a very small proportion of the SNPs.
Three loci (VC0147, VC0437, and VC1650) on the large chromosome were more stable (9 – 11 ) and are likely to be considered the best loci for estimating across distances, especially because of our observation of large differences in genotypes between locations 50 miles apart in rural Bangladesh (9 ).
Where a best two-locus through N-locus model is found by MDR or MDR-PDT, the genotypes at the model loci are determined to be high or low-risk by individual assessment of each model locus by MDR or MDR-PDT.
For DROMPA, we used three mapping parameter options: '-m1' (uniquely mapped reads), '-m10' (all mapped loci per read mapped ≤10 times) and '-k1' (best matched locus per all multiple mapped reads).
Upon incorporation of all possible markers, the FLIPS option was used to ascertain the best possible locus order by looking at all possible permutations for up to six adjacent loci within the resulting map.
