Output - ID (Insertions and Deletions)
This page provides detailed information about Insertion and Deletion (ID/Indel) output files.
Overview
ID matrices classify small insertions and deletions based on size, sequence context, and repeat/microhomology status.
Output Files
| File | # of Sequences | Description |
|---|---|---|
| test.ID28.all | 28 | Basic indel classification |
| test.ID83.all | 83 | Extended classification |
| test.ID415.all | 415 | With TSB categories |
| test.ID8628.all | 8628 | Complete sequence information |
ID-28
The ID28 file provides basic classification of insertions and deletions.
Categories
| Category | Description | Rows |
|---|---|---|
| 1:Del:C:0-5 | 1bp deletion of C in homopolymer length 0-5+ | 6 |
| 1:Del:T:0-5 | 1bp deletion of T in homopolymer length 0-5+ | 6 |
| 1:Ins:C:0-5 | 1bp insertion of C in homopolymer length 0-5+ | 6 |
| 1:Ins:T:0-5 | 1bp insertion of T in homopolymer length 0-5+ | 6 |
| long_Del | >1bp deletions at repeat regions | 1 |
| long_Ins | >1bp insertions at repeat regions | 1 |
| MH | Microhomology-mediated deletions | 1 |
| complex | Complex indels | 1 |
Example: 1:Del:C:3 corresponds to a deletion of C in a sequence N[C]CCCN (homopolymer of 4 C's).
ID-83
ID-83 extends ID-28 by further categorizing repeat and microhomology indels.
Long Deletions/Insertions at Repeats
| ID-28 Category | ID-83 Categories |
|---|---|
| long_Del | 2:Del:R:0-5, 3:Del:R:0-5, 4:Del:R:0-5, 5:Del:R:0-5 |
| long_Ins | 2:Ins:R:0-5, 3:Ins:R:0-5, 4:Ins:R:0-5, 5:Ins:R:0-5 |
Microhomology
| ID-28 Category | ID-83 Categories |
|---|---|
| MH | 2:Del:M:1-5, 3:Del:M:1-5, 4:Del:M:1-5, 5:Del:M:1-5 |
Notation:
- X:Del:R:Y = Deletion of length X at repeat with Y repeat units
- X:Del:M:Y = Deletion of length X with Y bp microhomology
Example: 1:Del:C:1 corresponds to a deletion of C in sequence N[C]CN.
ID-415
ID-415 categorizes each ID-83 category into 5 transcriptional strand bias categories.
Calculation: 83 × 5 = 415 combinations
TSB Categories
| Category | Description |
|---|---|
| T | Transcribed strand |
| U | Untranscribed strand |
| N | Non-transcribed |
| B | Bidirectional |
| Q | Questionable |
Example: T:1:Del:C:5 corresponds to a deletion of C in homopolymer CCCCCC on the transcribed strand.
ID-8628
ID-8628 provides complete information about the indel sequence for indels at repetitive regions with length less than 6bp.
Format
| Pattern | Description |
|---|---|
| 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 at 2 repeat units |
This extended classification allows for more precise analysis of indel patterns.
File Extensions
| Extension | Description |
|---|---|
.all |
All mutations (default) |
.exome |
Mutations mapped to exome regions |
.region |
Mutations mapped to custom BED file regions |
.chrX |
Chromosome-specific mutations |