<h1> Insertions and Deletions, Indels (ID) </h1> @[toc](Quick Links) - [Using the Tool - **Output**][1] --- ## Overview ##  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. <h3> Indel Sample Plot </h3>  <br> ### ID-28 ### 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. ### ID-83 ### 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<br> 3:Del:R:0 - 3:Del:R:5<br> 4:Del:R:0 - 4:Del:R:5 <br> 5:Del:R:0 - 5:Del:R:5| | long_Ins | 2:Ins:R:0 - 2:Ins:R:5<br> 3:Ins:R:0 - 3:Ins:R:5<br> 4:Ins:R:0 - 4:Ins:R:5 <br> 5:Ins:R:0 - 5:Ins:R:5| | MH | 2:Del:M:1 - 5:Del:M:5 <br> 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. ### ID-415 ### 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 <br> U:4:Del:R:4 <br> N:4:Del:R:4 <br> B:4:Del:R:4 <br> 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. ### ID-8268 ### 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)| [1]: https://osf.io/s93d5/wiki/4.%20Using%20the%20Tool%20-%20Output/