Based on manually counting reads in IGV, it seems that coverage in IGV strictly displays the coverage of the reads and nothing more, with no consideration for the underlaying fragment of paired end sequencing data (particularly evident with viewing reads as pairs). Not only does the insert region get dropped from the coverage calculations, but overlapping pair mates are also double counted in the overlap region.
Due to splicing etc, accurate quantification of the fragment coverage is probably rather difficult with eukaryotes. With prokaryotes however, this should be possible. I was hoping that bamCoverage of the deepTools package would accomplish this, but it also seems to have some issues.
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bluskale •
It is not clear what you are asking. Are you asking whether a region bridged over a pair will be reported as covered (coverage increased by 1) even though none of the sequences of the pair covers that region?
That is exactly what I am asking.