Viewing Data | Viewing Run Data | View Run & Lane Metrics

View Run & Lane Metrics

The Run Summary 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.

Use this option if you want a quick breakdown of the statistics for a particular run.

1 Click the Runs icon.
2 Click the desired run.
3 From the Run Overview Page, select the Run Summary icon from the left navigation menu.

The following metrics are displayed in the top table, split out by read and total.

Table 7   Run Summary Metrics

Metrics

Description

Cycles

The number of cycles in the read.

Yield

The number of bases sequenced, which is updated as the run progresses.

Projected Total 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.

The following metrics are available in the Read tables, split out by lane.

Table 8   Read Tables Metrics

Metrics

Description

Tiles

The number of tiles per lane.

Density

The density of clusters (in thousands per mm2) detected by image analysis, +/- 1 standard deviation. 

Clusters PF

The percentage of clusters passing filtering, +/- 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.

Reads

The number of clusters (in millions).

Reads PF

The number of clusters (in millions) passing filtering.

%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.

Cycles Err Rated

The number of cycles that have been error-rated using PhiX, starting at cycle 1.

Aligned

The percentage that aligned to the PhiX genome.

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.

%Intensity Cycle 20

The corresponding intensity statistic at cycle 20 as a percentage of that value at the first cycle. 100%x(Intensity at cycle 20)/(Intensity at cycle 1).