View Run Metrics

The Run & Lane Metrics page has the overall statistics about the run. Use this option when you want to view information about the run, such as percent alignment, cycles, and densities.

The following metrics appear in the top table, Per Read Metrics:

Metric	Description
Cycles	The number of cycles in the read.
Yield	The number of bases sequenced, which is updated as the run progresses.
Projected Yield	The projected number of bases expected to be sequenced at the end of the run.
Aligned	The percentage of the sample that aligned to the PhiX genome, which is determined for each level or read independently.
Error Rate	The calculated error rate of the reads that aligned to PhiX.
Intensity Cycle 1	The average of the A channel intensity measured at the first cycle averaged over filtered clusters. For the NextSeq 500 System, the red channel is used.
%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 Per Lane Metrics table:

Metric	Description
Clusters PF	The percentage of clusters passing filtering, +/- 1 standard deviation.
%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.
Yield	The number of bases sequenced which passed filter.
Tiles	The number of tiles per lane.
Error Rate	The calculated error rate, as determined by the PhiX alignment. Select Subsequent columns display the error rate for cycles 1–35, 1–75, and 1–100.
Error Rate @cycle	The error rate for cycles 1–35, 1–75, and 1–100. Select the Error Rate value to view this metric.
Cycles Err Rated	The number of cycles that have been error-rated using PhiX, starting at cycle 1. Select the Error Rate value to view this metric.
Aligned	The percentage that aligned to the PhiX genome. Select the Error Rate value to view this metric.
Reads PF	The number of clusters (in millions) passing filtering.
Total Reads	The number of clusters (in millions). Select the Reads PF value to view this metric.
Density	The density of clusters (in thousands per mm2) detected by image analysis, +/- 1 standard deviation.
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. For MiSeq and NextSeq, RTA generates phasing and prephasing estimates empirically for every cycle. The value displayed here is therefore not used in the actual phasing/prephasing calculations, but is an aggregate value determined from the first 25 cycles. For most applications, the value reported is very close to the value that is applied. For low diversity samples or samples with unbalanced base composition, the reported value can diverge from the values being applied because the value changes from cycle to cycle.
Phasing Slope/Offset, Prephasing Slope/Offset	The best-fit slope and offset of the phasing/prephasing corrections, calculated from the entire read.
Intensity	The average of the A channel intensity measured at the first cycle averaged over filtered clusters.
Status	The QC status for the run. Select the QC status to view detailed QC results.