Since you specified '-O' option, which instructs featureCounts to assign the read to all its overlapping features (they are exons in this case since you specified '-f'), reads will be assigned to all their overlapping exons. That says a read will be counted multiple times if it overlaps multiple exons. You can see this in the assignment results for two of the exons:
ENSG00000223972 1 13221 14409 + 1189 4
ENSG00000223972 1 13225 14412 + 1188 4
If you do not specify the '-O' option, reads overlapping with multiple exons will not be counted. Thus, you possibly will get zero count for both the two exons above.
ENSG00000223972 1 13221 14409 + 1189 4
ENSG00000223972 1 13225 14412 + 1188 4
If you do not specify the '-O' option, reads overlapping with multiple exons will not be counted. Thus, you possibly will get zero count for both the two exons above.
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