we limit our scope to applications of NGS where aligned reads are considered to be a population sample. In this definition of deep sequencing, reads aligning to a given genomic position are each assumed to originate from an individual replicon, revealing a snapshot of the population’s genetic diversity.

Sequencing of populations, on the other hand, has the drawback that unless variants co-occur within a read length or read pair, it is difficult to reconstruct individual haplotypes and perform phylogenetic analysis.

This ability to detect low frequency variants is an important feature of deep sequencing, for example in the context of drug resistance.
深度测序对用于发现低频突变从而来分析耐药性。

Sequencing of populations, on the other hand, has the drawback that unless variants co-occur within a read length or read pair, it is difficult to reconstruct individual haplotypes and perform phylogenetic analysis.
深度测序对于构建单倍型和进化分析来说 就很困难。

either by simply considering physical linkage of SNVs within individual reads, or by using overlapping reads to reconstruct longer genome fragments, termed ‘haplotypes’.