Statistical Analyses
Descriptive statistics, a single factor analysis of variance (ANOVA),
and a linear regression were calculated in Microsoft Excel v16.16.20
using the data analysis add in. The ANOVA was performed on the quality
data (represented by the percentage of reads passing quality from
prinseq) compared against the sample types.
The program MicroDrop v1.01 (Wang & Rosenberg, 2012) was run to
evaluate the rates of allelic dropout within samples and across loci.
The program was run twice, once on the genotypes called directly by
CHIIMP based on the pooled data, and once on the genotypes determined by
our best practices, shown in the ‘Manually Processed Genotypes’ column
of Table 4. The program was run using the default parameters, and we did
not enforce Hardy-Weinberg Equilibrium on our data due to the low number
of alleles and samples. Individual replicates were not run on MicroDrop,
as the program is designed to work on non-replicated datasets, although
the pooled data had multiple replicates of each individual pooled prior
to library preparation.