Output from Identify Mispriming Events

Four outputs are produced from the Identify Mispriming Events tool:

Mispriming events

The mispriming events track includes the following annotations:

Primers

The primer track includes the following annotations:

Misprimed reads track

Each mispriming event is represented by two reads in the read mapping: A read with the sequence of the primer aligned to the mispriming site, and a read with the sequence of the mispriming site aligned to the primer design region. Primers with multiple mispriming events will have a read for each mispriming event aligned at the primer design region.

For mispriming events that potentially cause false positives in the non-primer part of the read, two additional reads are included in the read mapping: A read with the downstream sequence of the primer aligned to the downstream of the mispriming site, and a read with the downstream sequence of the mispriming site aligned to the downstream of the primer design region. The mismatches in these reads show the potential false positive variants that can arise from mispriming.

Report

The mispriming event report includes the following information: