Interpreting Color by Pair Orientation
The orientation of paired reads can be used to detect structural events including:
- inversions
- duplications
- translocations
By selecting Color alignments>by pair orientation, you can flag anomalous pair orientations in IGV.
Orientation is defined in terms of read-strand: left versus right, and first read versus second read of a pair.
(figure courtesy of Bob Handsaker)
These categories only apply where both mates map to the same chromosome.
Inversions
An inversion is a large section of DNA that is reversed in the subject genome compared to the reference genome.
When an inversion shows up in paired-end reads, the reads are distinctively variant from the reference genome.
This appears in IGV as shown below.
Inverted Duplication
When a large section of DNA is duplicated and inserted into the genome in a reversed configuration compared to the original sequence, this is called an inverted duplication.
There will be overlapping left and right reads, and there will likely be altered coverage depth/copy number.
This appears in IGV as shown below.
Tandem Duplication
When a large section of DNA is duplicated and inserted into the genome next to the original sequence, this is called a tandem duplication.
The reads will not only be duplicated, but also be arranged as shown below.
IGV will display this rearrangement as shown below.
Translocation on the Same Chromosome
When a large section of DNA is removed from one location and inserted elsewhere, that is a translocation.
Translocations on the same chromosome can be detected by color-coding for pair orientation, whereas translocations between two chromosomes can be detected by coloring by insert size.
