Box 1: Sequencing strategies in population genomics
Whole-genome resequencing (WGR) is one of several sequencing
technologies that can be used for population genomic analysis. Currently
the most common family of technologies for WGR is short-read sequencing,
where reads are aligned to an already-available reference genome. The
per-base pair error rate is approximately 0.31% for Illumina reads
(Schirmer, D’Amore, Ijaz, Hall, & Quince, 2016). Therefore, if rare
variants (those that occur in few individuals, and which differ from the
reference genome) need to be identified with high accuracy, high
sequence depth (i.e. , a relatively large average number of reads
that cover each base pair in the genome for each individual) may be
required, although this can also be achieved by sequencing large
population samples at low per-individual coverage. This may often be the
case when using demographic inference to estimate the timing of an
invasion event (see Part 3.1). In the example below, the sequence depth
at the locus highlighted in grey is 11X.