|
= |
complete, exact match of intron chain |
|
c |
contained in reference (intron compatible) |
|
k |
containment of reference (reverse containment) |
|
m |
retained intron(s), all introns matched or retained |
|
n |
retained intron(s), not all introns matched/covered |
|
j |
multi-exon with at least one junction match |
|
e |
single exon transfrag partially covering an intron, possible pre-mRNA fragment |
|
o |
other same strand overlap with reference exons |
|
s |
intron match on the opposite strand (likely a mapping error) |
|
x |
exonic overlap on the opposite strand (like o or e but on the opposite strand) |
|
i |
fully contained within a reference intron |
|
y |
contains a reference within its intron |
|
p |
possible polymerase run-on (no actual overlap) |
|
r |
repeat (at least 50% bases soft-masked) |
|
u |
none of the above (unknown, intergenic) |