Edit metrics

The Edit Metrics facet reports statistics regarding edits to the reference sequence for read ones and read twos. The report is delivered at under the edits key within the results.json file. You can easily examine the output of the general facet by using jq:

cat results.json | jq .edits

Overview

This facet tracks the number of edits between read ones and read twos. An edit is defined as an alignment match (designated as M in the CIGAR string) where the nucleobases between the reference and the record do not match.

Outputs

This facet has the following top-level keys,

Key	Description
read_one_edits	Number of records that have n edits (based on the histogram). Only records marked as being the first segment ("read one") are considered.
read_two_edits	Number of records that have n edits (based on the histogram). Only records marked as being the last segment ("read two") are considered.
summary	Contains summary metrics for this facet, including the mean number of edits for both read ones and read twos.

Read One/Two Edits

This histogram contains the number of records which contain n edits, where n is the bin number of the histogram. For example, if bin 2 has a value of 100000, then there are 100,000 records which had an edit count of 2.

Summary

Contains summary metrics for this facet, including the mean number of edits for both read ones and read twos.