Run Summary
The Run Summary page displays 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 Total—The number of bases sequenced. |
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Projected Total Yield—The projected number of bases sequenced at the end of the run. |
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Yield Perfect—The number of bases in reads that align perfectly, as determined by a spiked in PhiX control sample. If no PhiX control sample is run in the lane, this chart is not available. |
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Yield <=3 errors—The number of bases in reads that align with 3 errors or less, as determined by a spiked in PhiX control sample. If no PhiX control sample is run in the lane, this chart is not available. |
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Aligned—The percentage of the sample that aligned to the PhiX genome. |
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% Perfect [Num Cycles]—The percentage of bases in reads that align perfectly, as determined by a spiked in PhiX control sample, at the cycle indicated in the brackets. If no PhiX control sample is run in the lane, this chart is not available. |
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% <=3 errors [Num Cycles]—The percentage of bases in reads that align with 3 errors or less, as determined by a spiked in PhiX control sample, at the indicated cycle. If no PhiX control sample is run in the lane, this chart is not available. |
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Error Rate—The calculated error rate, as determined by the PhiX alignment. |
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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. |
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%Q>=30 —The percentage of bases with a quality score of 30 or higher, respectively. This chart is generated after the 25th cycle, and the values represent the current 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 density of clusters (in thousands 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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Reads—The number of clusters (in millions). |
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Reads PF—The number of clusters (in millions) passing filtering. |
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%Q>=30—The percentage of bases with a quality score of 30 or higher, respectively. This chart is generated after the 25th cycle, and the values represent the current cycle. |
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Yield—The number of bases sequenced. |
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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. |
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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. |
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