If we use as an example a 50bp bin, of which only one single bp is covered by 1 read, and assume that 1 read coverage has a value of 5. For

--skipNAs

the value of the bin would be calculated as 1(bp) *5 = 5 (49 positions are skipped/ignored). For

0-value

bins, the value of the bin would be calculated as [1(bp) * 5 + 49(bp) * 0] / 50 = 0.1