What does -5 mean in bedtools genomecov?

[Rhine86]

help message shows that -5 mean "calculate coverage of 5' positions instead of entire interval", but I don't know what's 5' position exactly means?

ZHANG Yan

[FatihSarigol]

Thanks for this question! I am wondering exactly the same thing at the moment. Did you find an answer to it? I look into my bam file with tview, but the numbers genomecov -5 reports for certain positions doesn't make perfect sense to me, I can't see any pattern about what it exactly counts..

[cmatKhan]

I'm curious to know how this setting treats soft clipping -- is it 5' of the alignment, or the query?