Run report metrics after alignment

To assess the sequencing run when an accurate reference is available, you can review the quality metrics for aligned reads. Reads are aligned to a reference genome sequence. The following post-alignment metrics are provided in the run report.

Number	Metric	Description
1	Total Aligned Bases	The number of filtered and trimmed aligned base pairs reported in the output BAM file that are aligned to the reference sequence, excluding the library key, barcodes, and 3' adapter sequences.
2	Reference Coverage	The ratio of the total aligned bases divided by the number of bases in the reference sequence. Reference coverage does not account for enrichment done to selectively amplify a subset of the reference sequence.
3	Alignment plot	A plot of the number of aligned reads (blue) and unaligned (purple) by position in an aligned sequence.
4	Total Reads	The total number of reads after filtering.
5	Aligned Reads	The number of reads that align to the reference sequence expressed as a total count and percentage of the total aligned reads.
6	Unaligned Reads	The number of reads that do not align to the reference sequence expressed as a total count and percentage of the total reads.
7	Mean Raw Accuracy 1x	The mean raw accuracy across each individual base position in a read calculated as 1− (total errors in the sequenced base) / total bases sequenced.
8	AQ17 Total Bases	The total number of bases over all positions that align with an error rate of 2% or less.
9	Total Number of Bases (bp)	The total number of bases over all positions that align with a given error rate. (AQ17 ≤2% error rate, AQ20 ≤1% error rate, Perfect = no measurable error)
10	Mean Length (bp)	The average length, in base pairs, for aligned reads at a given error rate. (AQ17 ≤2% error rate, AQ20 ≤1% error rate, Perfect = no measurable error)
11	Longest Alignment (bp)	The maximum sequence read length for a given error rate. (AQ17 ≤2% error rate, AQ20 ≤1% error rate, Perfect = no measurable error)
12	Mean Coverage Depth (x)	The ratio of the total aligned bases at a given error rate to the size of the target region. (AQ17 ≤2% error rate, AQ20 ≤1% error rate, Perfect = no measurable error)