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This question already has an answer here:

What does it mean when N-Fold coverage of read of sequence? Details will be much appreciated if a link provider with brief explanation.

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marked as duplicate by AliceD, MattDMo, March Ho, James, WYSIWYG Mar 15 '16 at 6:52

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  • $\begingroup$ What you're asking is a little unclear to me...I don't know if this is what you're looking for, but typically, the fold coverage of a read represents the number of times that particular read was sequenced in a given run. $\endgroup$ – Forest Mar 9 '16 at 18:56
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Fold coverage is often derived with respect to a genomic locus, not a read. In sequencing experiments, fold coverage of a genomic loci (coordinate along a reference assembly) will be the number of aligned reads that overlap the position.

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    $\begingroup$ It could also be the average coverage of a genome based on number of reads, read length and expected genome size. $\endgroup$ – skymningen Mar 10 '16 at 13:26
  • $\begingroup$ Thank you for the additional detail. Absolutely, on a genome level the fold coverage is computed as: number of reads * read length / genome size, and genome size here be either the true genome size or the size of the fraction of genome that is captured for sequencing. $\endgroup$ – Noushin Mar 10 '16 at 16:09
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N-fold coverage usually refer to the average number of reads spanning across a particular region of interest. For example, if you are interested in a gene and would like to know how confident your data is, you may look for the coverage.

There is no absolute definition on how N-fold coverage is calculated. The most common method is to get the arithmetic average per base.

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