General metrics

The General Metrics facet reports general statistics about the records contained within the file. The report is delivered at <output_prefix>.summary.json as a JSON file with the following top-level keys.

Key	Description
record_metrics	Metrics regarding record counts, including total number of records, unmapped records, duplicate records, and the designation of records (primary, secondary, supplementary).
summary	Contains summary metrics for this facet, including duplication record percentage and unmapped record percentage.

Record metrics

Record metrics comprise multiple general counting metrics regarding records. Many of these counts are simply cycling through the reads and counting up reads with particular flags. The current set of record metrics collected include:

• Total. The total number of records within the file.
• Unmapped. The total number of unmapped records within the file.
• Duplicate. The total number of duplicate records within the file.
• Designation. The total number of primary, secondary, and supplementary records in the file respectively.

Summary

Summary metrics are generally percentages that are of interest to users. The current set of summary metrics collected include:

• Duplication percentage. The percentage of records that are marked as duplicate in the file.
• Unmapped percentage. The percentage of records that are marked as unmapped in the file. This also allows one to trivially calculate the mapped percentage.