Review alignment metrics
The secondary pipeline aligns the run to the reference. Here you can see how many bases align to the reference.
- In the Data tab, click Completed Runs & Reports, then select a run of interest.
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Scroll down to the Aligned to reference name section, then review Total Aligned Bases, Reference Coverage, Mean Raw Accuracy, and Total Bases Alignment Quality.
For more information on these metrics, see Run report metrics on aligned reads
