I'm having some trouble in understanding the output of MultiBreak-SV, specifically the file processed by the quick-post-process.py script. My question is, why are the ranges for both left breakpoints and right breakpoints reported in each line, specifically for the SV types I+ and I- ? Are they both valid, or only the left range for I+ (or the right range for I-) is valid?
The following is my understanding, so if you are aware of my my question, you can skip this and answer my question directly.
I'm aware that IR stands for reciprocal inversion (both ++ and --), I+ stands for the inversion that is ++ side only, and I- stands for the inversion that is -- side only. But what do the ++ and -- side mean exactly?
To my knowledge, this representation is derived from the cluster files from GASV. In the manual of GASV, there is a sentence:
This variant is a reciprocal inversion (Type = IR). Among the 4 PRs at least one is in the ++ orientation (contains the left breakpoint) and one in the -- orientation (contains the right breakpoint)
So my understanding is that ++ means the left breakpoint, and -- means the right breakpoint. Since both of the ranges appear in the I+ and I- lines, does this mean that only the range of the left breakpoint for I+ (or the range of the right breakpoint I-) is valid in the output file?
I have a simulation result for E. coli that has 4641652 bp. But after running MultiBreak-SV, one of the result is c869 0.0000 0.0000 I+ 1 727223-727680 1 4045275-4045732 1 longread_10436_0.10-1.10. If both ranges of the breakpoints should be considered in my downstream analysis, it will mean that almost the whole genome is inverted. So if my previous understanding is wrong, how to explain this one?
Thanks in advance.
