Summary Metrics

After cycle 25 of Read 1, review the following run metrics to determine whether the flow cell is overclustered. Metrics are available from the Summary tab in Run Metrics Software or the Metrics tab in Analysis Software (AS).

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Aligned—Check whether the percent of reads that aligned to PhiX is close to the percent spiked in, which is ideal. A mismatch can indicate that the starting concentration of the library was misestimated. For example, for a 10% PhiX spike-in:

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A 1% PhiX alignment indicates an unexpectedly high library concentration, generally with high cluster density or overclustering.

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A 50% PhiX alignment indicates an unexpectedly low library concentration, generally with low cluster density or underclustering.

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Clusters PF—Check whether the percentage of clusters passing filter is sufficiently high.

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Density—Check whether the density value exceeds the range Illumina recommends for the system and reagent kit version. See Recommended Cluster Densities.