Quality Metrics Summary
The Summary link leads to tables with basic data quality metrics summarized per lane and per read. All the statistics are given as means and standard deviations over the tiles used in the lane. The following metrics are displayed in the top table, split out by read and total:
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Yield—The number of bases sequenced, in gigabases. |
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Error Rate—The calculated error rate, as determined by the PhiX alignment. |
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Aligned—The percentage of the sample that aligned to the PhiX genome. |
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Intensity Cycle 1—The average of the four intensities (one per channel or base type) measured at the first cycle averaged over filtered clusters. |
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Intensity Cycle 20—The corresponding intensity statistic at cycle 20 as a percentage of that at the first cycle. |
The following metrics are available in the Read tables, split out by lane:
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Tiles—The number of tiles per lane. |
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Density—The number of clusters per mm2 detected by image analysis. |
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Clusters PF—The percentage of clusters passing filtering. |
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Phas./Prephas.—The value used by RTA for the percentage of molecules in a cluster for which sequencing falls behind (phasing) or jumps ahead (prephasing) the current cycle within a read. |
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Cycles Err Rated—The number of cycles that have been error rated starting at cycle 1. |
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Aligned—The percentage of the sample that aligned to the PhiX genome. |
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Error Rate—The calculated error rate, as determined by the PhiX alignment. Subsequent columns display the error rate for cycles 1–35, 1–75, and 1–100. |
Metric plots are available when you select the Details button.