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Interpreting Color by Insert Size

The inferred insert size can be used to detect structural variants, such as:

  • deletions
  • insertions
  • inter-chromosomal rearrangements

IGV uses color coding to flag anomalous insert sizes. When you select Color alignments>by insert size in the popup menu, the default coloring scheme is:

  • for an insert that is larger than expected
  • for an insert that is smaller than expected
  • for paired end reads that are coded by the chromosome on which their mates can be found

Deletions

A deletion is a large section of DNA that is absent in the subject genome compared to the reference genome.

 

The "expected" insert size is the insert size obtained in sequencing the subject genome.  The "inferred" insert size is the insert size that would result in the reference genome, assuming the same pair of reads.

 In the case of a deletion, the inferred insert size is GREATER THAN the expected insert size.

Reads that are colored red have larger than expected inferred sizes, and therefore indicate deletions.

Insertions

An insert is a large section of DNA that is present in the subject genome but is not in the reference genome.

The "expected" insert size is the insert size obtained in sequencing the subject genome.  The "inferred" insert size is the insert size that would result in the reference genome, assuming the same pair of reads.

So, in the case of an insert, the inferred insert size is LESS THAN the expected insert size.

The maximum size detectable by insert size anomaly is limited by the size of the fragments.  They must be long enough to span the insertion and include sequence on both ends that are mapped to the reference.  The maximum detectable size is approximately equal to:

fragment length - (2x read length)

Detection of this event is more likely with larger fragment libraries, such as Illumina mate-pair (not paired-end) and SOLID.

Reads that are colored blue have smaller than expected inferred sizes, and therefore indicate insertions.

Inter-chromosomal Rearrangement

IGV codes inserts for inter-chromosomal rearrangements.  For instance, in this case, one end is on chromosome 1 and the other is on chromosome 6.