Visualization histograms
This sample demonstrates an insertion identified using MELT and whole-genome sequencing data.
There are two types of vertical rectangle:
- A dark blue rectangle indicates where the mobile element sequence begins (
)
- A light blue rectangle shows the region containing target site duplications (MELT only) (
)
- Reference Genome: This refers to the reference genome initially used to align the reads such as hg19
- Mobile Element: This is a novel element that has been inserted into the reference genome
- Junction Region: This is the dividing point between the reference genome sequence and the sequence of the mobile element
There are two junction regions for whole-genome sequencing data, while there is only one for TIPseq. In TIPseq, only the 3' end of the LINE-1 mobile element is sequenced.
Individual reads are binned into histograms depending on their orientation relative to the mobile element.
IMAGE OF READS ALIGNMENTS
Each configuration is colored differently to make it easy to distinguish
Possible read configurations:
| Configuration | Description | Color |
|---|---|---|
| Genome / Genome | Both reads align to the reference genome on the same side of the insertion | |
| Genome / Genome (bridging) | One read aligns to the reference genome on the 5' end of the insertion, and the other aligns to the reference genome on the 3' end | |
| Genome / Junction | One read aligns to the reference genome, and its mate overlaps with the junction region on the same side of the insertion | |
| Genome / Junction (bridging) | One read aligns to the reference genome, and its mate overlaps with the junction region on the opposite side of the insertion | |
| Genome / Mobile | One read aligns to the reference genome, and its mate aligns with the sequence of the mobile element |
|
| Genome / Unmapped | One read aligns to the reference genome and its mate is unmapped | |
| Junction / Mobile | One read overlaps the junction region, and its mate aligns with the mobile element | |
| Junction / Junction | Both reads overlap the same junction region | |
| Junction / Junction (bridging) | One of the reads overlaps the 5' junction region, and the other overlaps the 3' junction region | |
| Junction / Unmapped | One of the reads overlaps the junction region, and the other is unmapped | |
| Mobile / Mobile | Both of the reads align to the mobile element | |
| Mobile / Unmapped | One read aligns to the mobile element, and the other is unmapped |
Any histogram that overlaps with the mobile element is given diagonal white stripes.