Help!! Interpret MoDIL results.

[minhduc]

Hi all,

I have been trying to find indels using MoDIL, but have problems interpreting the results. According to the README file

Results format is:

- Cluster ID: Unique ID for each indel prediction
- Chromosome: Chromosome where the indel is located.
- Start location: Start location of indel
- End location: End location of indel
- Insertion flag: If it is 1, the row means insertion, deletion otherwise.
- Deletion flag: If it is 1, the row means deletion, insertion otherwise.
- Size of indel: If it is negative it means deletion, insertion otherwise.
(ex) -300 => 300bp deletion
(ex) 12 => 12bp insertion
- P value: P-value of the indel prediction
- Likelihood of homozygosity: If it is homozygous, it is close to 1.
- Number of matepairs that support indel
- Number of matepairs that support no indel: If it is zero, the indel
is homozygous

and a sample output extracted from the predicted INDELs in Yoruban genome, provided in the MoDIL website (http://compbio.cs.toronto.edu/modil/)

1.0 chr1 218651814 218652002 1 0 75.0 0 1e-09 21220038 0 47 0 25 36 218651906 218651972
1.0 chr1 102759676 102760211 0 1 -329.0 0 1e-09 10323514 0 67 0 32 37 102759712 102760037

My interpretation of these results is that there are a 75pb insertion starting at pos 218651814 and ending at pos 218652002, and a 329pb deletion between 102759676 and 102760211. What I don't understand is, in the first line, how an insertion of size 75bp can start at 218651814 and end at 218652002 (i.e., 188 bp apart)? Likewise, in the second line, how a deletion from 102759676 to 102760211 (535 bp in between) can be a 329pb deletion?

Could anyone please help to explain or to correct my interpretation?

Thanks
MD