Discrepancy between coverage between Bam file and epinano/tombo site output?

[smk5g5]

Hi,

I am trying to compare how coverage varies with regard to the epi-transcriptomic modification. When comparing the output of epinano/tombo (generated from the master of pores pipeline) I noticed there is a discrepancy between the coverage represented in the file which has modification information and the coverage when calculated using genomeCoverageBed command from Bedtools.

I was wondering why is that. e.g. the sample_name*.tsv.per.site.var.csv.gz file which looks like.

#Ref,pos,base,cov,q_mean,q_median,q_std,mis,ins,del
ENST00000291700.9,199,A,332.0,19.21687,20.00000,8.24811,0.0030120481927710845,0.006024096385542169,0.0

has coverage of "332.0" here. But in the bedtools output it shows to be :-

ENST00000291700.9 199 469
Where 199 is the position and 469 is the read depth/coverage.

I was wondering how and why the values above are different. Are they calculated differently or do they mean different things?

Kindly let me know. Thank you!