Adapter Metrics File

The adapter metrics file (Adapter_Metrics.csv) reports the number of bases detected to belong to adapters for each read per sample ID. This information allows for the detection of the genomic yield by subtracting the count of adapter sequence bases. Bases that match adapter sequences can be removed (trimmed), or replaced with N(s) (masked), from the output by configuring the [BCLConvert_Settings] section.

Each Read Group is reported, defined as the unique combination of lane, sample ID, and index pair. The columns are left blank when they do not apply to the given sample. For a run without adapters, the file is output with only the header. The headings are as follows:

Heading	Description
Lane	Lane number.
Sample_ID	Sample ID.
index	The Index 1 (i7) index adapter sequence.
index2	The Index 2 (i5) index adapter sequence.
R1_AdapterBases	Number of bases trimmed or masked from the corresponding read for the corresponding and sample. Includes Ns that replace base pairs according to the MaskShortReads setting.
R1_SampleBases	Number of PF bases included in the corresponding read not belonging to an adapter for the corresponding and sample.
R2_AdapterBases	Number of bases trimmed or masked from the corresponding read for the corresponding sample, including Ns that replace base pairs according to the MaskShortReads setting.
R2_SampleBases	Number of PF bases included in the corresponding read not belonging to an adapter for the corresponding and sample.
# Reads	Number of reads.