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 sizes. 

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.