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This output folder returns files containing all the insertions and deletions found within the samples. If no files are returned, this means no insertions or deletions were found.
The test.ID28.all file identifies all 1 bp (C and T only) insertions and deletions from homopolymer length 1 to 6+, the >1bp deletions and insertions as repeats, and all other indels in the microhomology category and categorizes each by length.
The generated plot above gives a visual for how each indel is categorized and returned.
| Mutation Type | Sample 1 (PD10001a) | Sample 2 (PD10011a) | ..... |
|---|---|---|---|
| 6 rows for 1:Del:C:0 to 1:Del:C:5 | frequency of each deletion of C in sample 1 | frequency of each deletion of C in sample 2 | .... |
| 6 rows for 1:Del:T:0 to 1:Del:T:5 | frequency of each deletion of T in sample 1 | frequency of each deletion of T in sample 2 | .... |
| 6 rows for 1:Ins:C:0 to 1:Ins:C:5 | frequency of each insertion of C in sample 1 | frequency of each insertion of C in sample 2 | .... |
| 6 rows for 1:Ins:C:0 to 1:Ins:C:5 | frequency of each insertion of T in sample 1 | frequency of each insertion of T in sample 2 | .... |
| long_Del (repeat units) | frequency of each long deletion in sample 1 | frequency of each long deletion in sample 2 | .... |
| long_Ins (repeat units) | frequency of each long insertion in sample 1 | frequency of each long insertion in sample 2 | .... |
| MH (microhomology) | 0 | 0 | |
| complex | 0 | 0 |
 The above image is a screenshot of the generated file. Here, on line 5, 1:Del:C:3 corresponds to a deletion of C in a sequence N[C]CCCN where N is represents any nucleotide A, T, or G to give NCCCN.
The test.ID83.all file further categorizes each unique repeat and microhomology indel found.
| test.ID28.all | test.ID83.all |
|---|---|
| long_Del | 2:Del:R:0 - 2:Del:R:5 3:Del:R:0 - 3:Del:R:5 4:Del:R:0 - 4:Del:R:5 5:Del:R:0 - 5:Del:R:5 |
| long_Ins | 2:Ins:R:0 - 2:Ins:R:5 3:Ins:R:0 - 3:Ins:R:5 4:Ins:R:0 - 4:Ins:R:5 5:Ins:R:0 - 5:Ins:R:5 |
| MH | 2:Del:M:1 - 5:Del:M:5 2:Ins:M:1 - 5:Ins:M:5 |
 Here, on line 3, 1:Del:C:1 corresponds to a deletion of C in a sequence N[C]CN where N is represents any nucleotide A, C, or G to give NCN.
The test.ID415.all file categorizes each identified indel from test.ID83.all into the 5 transcriptional strand bias categories {T, U, N, B, Q}.
83 x 5 = 415 combinations
For example, a category in test.ID83.all would be further categorized into the following in test.ID415.all.
| test.ID83.all | test.ID415.all |
|---|---|
| 4:Del:R:4 | T:4:Del:R:4 U:4:Del:R:4 N:4:Del:R:4 B:4:Del:R:4 Q:4:Del:R:4 |
 The above image is a screenshot of the generated file. Here, on line 7, T:1:Del:C:5 corresponds to a deletion of C in a sequence N[C]CCCCCN where N is represents any nucleotide A, C, or G to give NCCCCCN. on the transcribed strand.
The test.ID8268.all file extends the categorization from the ID-83 matrix by providing complete information about the indel sequence for indels at repetitive regions with length less than 6bp.
| test.ID8268.all | |
|---|---|
| 2:Del:TA:5 | Deletion of length 2 with sequence TC or GA (reverse complement) |
| 5:Ins:CCATC:2 | Insertion of length 5 with sequence CCATC or GATGG (reverse complement) |