Metrics Output

The demultiplex statistics file (Demultiplex_Stats.csv) provides the number of passing filter reads that are assigned to each sample in the sample sheet the set of undetermined reads treated as one sample. The file also contains information about the quality scores of bases in the passing filter reads assigned to each sample. For each sample ID in each lane, the following information is provided:

•

Number of reads

•

Number of perfect index reads

•

Number of index reads with one mismatch

•

Number of ≥ Q30 bases (passing filter)

•

Mean quality score (passing filter)

The index hopping metrics file (Index_Hopping_Counts.csv) contains the number of reads for each expected and hopped index for unique, dual index runs. The count is only reported for Unique Dual Indexes (UDI) per lane, where no barcode collision is detected in either index. For index hopping metrics to be output for the given lane, each pair of entries within each index must have a distance between bases of at least 2n+1, where n is the barcode mismatch tolerance specified for the index.

For nonindex runs, single index runs, or lanes that do not contain UDIs, the file is output with only the header.

The index metrics out file (IndexMetricsOut.bin) is a binary file that contains index statistics for each sample and index combination per lane provided to BCL Convert in the sample sheet. The content of the file is documented as follows:

•

Byte 0: file version number (2)

•

The remaining bytes represent records, which are composed of the following information:

–

2 bytes—Lane number (uint16)

–

4 bytes—Tile number (uint32)

–

2 bytes—Read number (uint16)

–

2 bytes—indexLength, the length in bytes of index name (uint16)

–

indexLength bytes—String representing index name

–

8 bytes—Number of occurrences of index (uint64)

–

2 bytes—sampleLength, the length in bytes of the sample name (uint16)

–

sampleLength bytes—String representing sample name

–

2 bytes—projectLength, the length in bytes of the project name (uint16)

–

projectLength bytes—String representing project name

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 and defined as the unique combination of lane, sample ID, and index pair. The columns are left blank if they do not apply to the given sample. For a run without adapters, the file is output with only the header. The following headings are present in the Adapter Metrics File:

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.