coveragebed problem

[Daytwa]

I am having trouble with the histogram option in coveragebed. I want to compare coverage of my uniquely aligned RNA-seq reads (list A) to a bed file of repeats (list B). When I run this comparison using the default command everything is fine:

bedtools coverage -abam unique.bam -b Repeats.bed > unique_repeats.bed

chrY 90737061 90737317 - IMPB_01 Satellite Satellite 0 0 256 0
chrY 90737327 90737430 + RLTR31D_MM LTR ERVK 0 0 103 0
chrY 90737435 90737736 - IMPB_01 Satellite Satellite 93 106 301 0.3521595

When I run this comparison with the -hist option I get some seemingly strange results:

bedtools coverage -hist -abam unique.bam -b Repeats.bed > unique_repeats.bed

90737061 90737317 - IMPB_01 Satellite Satellite 0 256 256 1
90737327 90737430 + RLTR31D_MM LTR ERVK 0 103 103 1
90737435 90737736 - IMPB_01 Satellite Satellite 0 195 301 0.6478406
90737435 90737736 - IMPB_01 Satellite Satellite 1 2 301 0.0066445
90737435 90737736 - IMPB_01 Satellite Satellite 5 1 301 0.0033223
90737435 90737736 - IMPB_01 Satellite Satellite 8 1 301 0.0033223
90737435 90737736 - IMPB_01 Satellite Satellite 36 1 301 0.0033223
90737435 90737736 - IMPB_01 Satellite Satellite 43 2 301 0.0066445
90737435 90737736 - IMPB_01 Satellite Satellite 44 49 301 0.1627907
90737435 90737736 - IMPB_01 Satellite Satellite 49 50 301 0.166113

At IPMPB_01 no reads in A overlap B but 100% of bases in B are listed as covered. This happens for all instances in which no reads in A overlap B (see 90737327 90737430 + RLTR31D_MM)

When there is overlap the bedtools prints several more lines of information but I can't make sense of it. In example at 90737435 90737736 - IMPB_01 the first line says that one read covers two bases while on the next line 5 reads cover one base and so on. In fact several lines state that many reads cover only one base.

Again this only happens when the histogram function is active. What am I missing here?