Editing Shotgun sequencing (section)

===Coverage===
{{main|Coverage (genetics)}}
Coverage (read depth or depth) is the average number of reads representing a given [[nucleotide]] in the reconstructed sequence.  It can be calculated from the length of the original genome (''G''), the number of reads(''N''), and the average read length(''L'') as <math>N\times L/G</math>.  For example, a hypothetical genome with 2,000 base pairs reconstructed from 8 reads with an average length of 500 nucleotides will have 2x redundancy. This parameter also enables one to estimate other quantities, such as the percentage of the genome covered by reads (sometimes also called coverage). A high coverage in shotgun sequencing is desired because it can overcome errors in [[base calling]] and assembly. The subject of [[DNA sequencing theory]] addresses the relationships of such quantities.

Sometimes a distinction is made between ''sequence coverage'' and ''physical coverage''. Sequence coverage is the average number of times a base is read (as described above). Physical coverage is the average number of times a base is read or spanned by mate paired reads.<ref name="MeyersonFig1">{{cite journal |last1= Meyerson |first1= M. |last2= Gabriel |first2= S. |last3= Getz |first3= G. |doi= 10.1038/nrg2841 |title= Advances in understanding cancer genomes through second-generation sequencing |journal= Nature Reviews Genetics |volume= 11 |issue= 10 |pages= 685–696 |year= 2010 |pmid= 20847746|s2cid= 2544266 }}</ref>