Mapping

Read-Level Metrics

Metric	Description
Total input reads	Total number of input reads
QC-failed reads	Total number of reads failing one or more quality checks
% QC-failed	Percentage of reads failing one or more quality checks
Unique reads	Total number of unique reads
% Unique	Percentage of reads that are unique
Mapped reads	Total number of mapped reads, adjusted for filtered and excluded targets
% Mapped	Percentage of reads that are mapped, adjusted for filtered and excluded targets

Base-Level Metrics

Metric	Description
Total Bases	Total number of input bases
Mapped R1	Total number of mapped bases on R1
% Mapped R1	Percentage of R1 bases mapped
% Q30 R1	Percentage of R1 bases with phred quality score >=30

Deduplication

The deduplication bar chart reflects the ratio of unique and deduplicated reads.

Read MAPQs

The read MAPQs bar chart reflects the percent of reads in various categories of phred quality score (Q0-Q10, Q10-Q20, Q20-Q30, Q30-Q40, Q40+).