Глубина секвенирования (sequencing depth) – при получении сырых геномных данных, каждый участок генома оказывается (чаще всего) пройденным несколько раз. Количество раз, которое был отсеквенирован каждый нуклеотид, называется глубиной покрытия и обычно описывается как 10Х, 20Х, 50Х и т.д. Глубина покрытия позволяет выявить возможные ошибки считывания нуклеотидов на машины и определить истинно полиморфные позиции в геноме.

Покрытие (coverage) – в настоящее время понятие покрытие используется как минимум в трех значениях
- Теоретическая глубина секвенирования – рассчитывается по формуле:
(общее число полученных ридов * длина рида ) / теоретическая длина генома
- Теоретический или эмпирический размах покрытия собранного генома, рассчитывается как:
размер собранного генома / теоретическая длина генома
- Эмпирическая глубина покрытия, рассчитывается как:
(общее число полученных ридов * длина рида ) / размер собранного генома

http://www.phylogenetics.ru/lang/ru/2014/02/assemblydictiona...

Coverage now appears to have 3 meanings:

- the theoretical "fold-coverage" of a shotgun sequencing experiment: number of reads * read length / target size
- the theoretical or empirical "breadth-of-coverage" of an assembly: assembly size / target size
- the empirical average "depth-of-coverage" of an assembly: number of reads * read length / assembly size

(1) and (3) are not the same because of sequencing error & unclonable/unmappable regions of the genome. Lander-Waterman theory deals with the relationship between (1) and (2).

https://www.biostars.org/p/638/

Histograms to Depict Sequencing Coverage Range and Uniformity

Coverage histograms are commonly used to depict the range and uniformity of sequencing coverage for an entire data set. They illustrate the overall coverage distribution by displaying the number of reference bases that are covered by mapped sequencing reads at various depths. Mapped read depth refers to the total number of bases sequenced and aligned at a given reference base position (note that "mapped" and "aligned" are used interchangeably in the sequencing community).

In an NGS coverage histogram, the read depths are binned and displayed on the x-axis, while the total numbers of reference bases that occupy each read depth bin are displayed on the y-axis. These can also be written as percentages of reference bases.
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Evaluating Next-Generation Sequencing Coverage

The following metrics are commonly used to evaluate NGS coverage:

Inter-Quartile Range (IQR): The IQR is the difference in sequencing coverage between the 75th and 25th percentiles of the histogram. This value is a measure of statistical variability, reflecting the non-uniformity of coverage across the entire data set. A high IQR indicates high variation in coverage across the genome, while a low IQR reflects more uniform sequence coverage. In the histograms above, the lower IQR indicates that the histogram on the left has better sequencing coverage uniformity than that on the right.

Mean (Mapped) Read Depth: The mean mapped read depth (or mean read depth) is the sum of the mapped read depths at each reference base position, divided by the number of known bases in the reference. The mean read depth metric indicates how many reads, on average, are likely to be aligned at a given reference base position.

Raw Read Depth: This is the total amount of sequence data produced by the instrument (pre-alignment), divided by the reference genome size. Although raw read depth is often provided by sequencing instrument vendors as a specification, it does not take into account the efficiency of the alignment process. If a large fraction of the raw sequencing reads are discarded during the alignment process, the post-alignment mapped read depth can be significantly smaller than the raw read depth.

http://www.phylogenetics.ru/lang/ru/2014/02/assemblydictiona...