Hello, I tried using this tool today after inputting a bed file containing
1509 intervals of 100 bp each, spread across all 22 autosomes.

First of all, despite the fact that my input file contained intervals for
22 chromosomes, the value of "allCoverage" seemed to be the same as the
value of the coverage of that table only for chr1. I was not really sure
about the tableRegionCoverage column, as for most of the autosomes I had
input data spread throughout the chromsome with points a few Mb away from
either end, but I was getting a value in this column only about 1/3 of what
I get when downloading the data directly from UCSC and summing the interval

There were also many cases where nrCoverage > allCoverage, even when I
reduced each input genomic interval to only 1 bp to avoid redundancy in the
input file. Based on these descriptions of the columns I would expect
allCoverage >= nrCoverage at all times.

Just wondering if you could clarify what these columns are supposed to mean
or how to reconcile these apparent inconsistencies.
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