We calculated a metric to reflect the potential of elephants to cross unprotected roads called Proportion of Road Crossings (PRC) (Table 1), as the proportion of 1000 randomly generated CRWs that crossed an unprotected road.
One SNP from TMC8 (rs17773854) was excluded from analysis, due to call proportion <0.90 and HWE P < 0.01.
The latter allows user-specified masking of contig positions based on read depth and base call proportion.
A consensus sequence of the aligned contigs is produced, which can be masked based on base call proportion and coverage depth; single nucleotide polymorphisms (SNPs) can be masked similarly using separate user specifications.
Recently, our group has proposed a method called proportion of unexpected correlations (PUC), which allows identifying and removing approximately half of false positive edges from a covariation network with no reduction in statistical power.
Aligned contig positions matching the reference were masked if fewer than five overlapping reads and less than 80% of all reads overlapping to form the contig at that position agreed with the reference; aligned positions called as SNPs were similarly masked, but required a minimum coverage depth of 20 aligned reads and 80% call proportion.
The graphs displayed in PIQA_report.html assess the clusters density per tile, the base-calls proportions per tile and per cycle, and finally the base-calls quality per tile and per cycle.
The interaction between software program (LAMP-LD or RFMix) and pair of ancestries was tested, while chromosome identifiers were specified as random effect, in order to adjust for the correlation between between different miss-call proportions on the same chromosome.
In order to standardize the variations, the stone non-cholesterol sterols were expressed as milligrams by stone weight and in terms of 10 × mmol of non-cholesterol sterol /mol of cholesterol (called proportions or ratios in the text).
Various problems which may occur in each step of the sample preparation and sequencing can be detected by an analysis of the variation of clusters density; base-call proportions; and base quality across cycles of the run, and across tiles and lanes of the flow cell.
