Outcomes For Mapping A Paired End

Basics

Paired end reads have an expected relative orientation (for example, FR are expected to map to opposite strands of the genome) and distance (for example, 500 bp +/- 100 bp apart).

Possible Mapping Outcomes

Proper Mapping

Reasonable alignment for the pair, which places both reads in the expected orientation and at the expected separation.

Most fragments should map like this.

Improper Pairs

Sometimes, the reads can be mapped individually, but don't map with the expected orientation and/or separation.

Clusters of reads that don't map as expected can suggested re-arrangements in the DNA sample being sequenced (such as insertions, deletions, inversions and translocations).

Only One End Maps

Sometimes, only one end can be matched to genome confidently. The other end might be low in quality, might overlap a sequence that is not present in the reference genome, or might be overlap a sequence re-arrangement such as deletion or insertion.

Clusters of reads such as this can be used to detect re-arrangements.

Sometimes the unmapped pair might be placed using a local alignment algorithm that allows for insertions and deletions in the neighborhood of the mapped read.