Metrics Tab

All statistics are provided as means and standard deviations over the tiles used in the lane. Cycle-based metrics, such as yield, error rate, and % Q ≥ 30, are calculated over fully corrected, usable cycles. The last cycle of every read is removed from all computations.

Using the icons in the upper-right corner, you can copy all tables to your clipboard, refresh metric results, download metric data, or save a picture of the current metric data.

The Cycle status above the top table displays a summary of the last cycle extracted, base called, Q-scored, and error rated for each tile.

The Read summary table displays the following metrics, divided by read level.

Metric	Description
Level	The sequencing read level.
Yield total	The number of non-N bases sequenced in gigabytes, 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 in gigabytes, which is updated as the run progresses.
Aligned %	The percentage of the passing filter clusters 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 channel intensity measured at the first cycle averaged over filtered clusters. For the NextSeq 1000/2000 and the NovaSeq X Series Systems, the green channel is used. For the MiniSeq, NextSeq 500, and NovaSeq 6000 Systems, the red channel is used. For the iSeq 100 sSstem, the first channel is used.
% Intensity Cycle 1	The average percentage of the channel intensity measured at the first cycle averaged over filtered clusters. For the NextSeq 1000/2000 and the NovaSeq X Series Systems, the green channel is used. For the MiniSeq, NextSeq 500, and NovaSeq 6000 Systems, the red channel is used. For the iSeq 100 System, the first channel is used.
% Q ≥ 30	The percentage of bases with Q30 or higher, respectively.
% Occupied	The percentage of clusters on a tile that are occupied by DNA sequence.

The following metrics are available in the read tables, divided by lane.

Metric	Description
Lane	The flow cell lane.
Tiles	The number of tiles per lane.
Density	The density of clusters (in thousands per mm²) detected by image analysis, +/- 1 standard deviation.
% Pass filter (PF)	The percentage of clusters passing filter.
Legacy phasing/prephasing rate	The value used by Real-Time Analysis for the rate (percentage per cycle) at which molecules in a cluster fall behind (phasing) or jump ahead (prephasing) during a read. This metric is an estimate from the first 25 cycles of each read.
Reads	The number of clusters (in millions).
Reads PF	The number of clusters (in millions) passing filter.
% Q ≥ 30	The percentage of bases with a quality score of 30 or higher.
Yield	The number of bases sequenced that passed filter.
Cycles error 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. The base unit is the error rate for a single tile. SAV averages the per-cycle error rate across all the relevant cycles for a tile before calculating these statistics.
Intensity cycle 1	The average of the A channel intensity measured at the first cycle averaged over filtered clusters. For the MiniSeq, NextSeq 500, and NovaSeq 6000 systems, the red channel is used. For the iSeq system, the first channel is used.
Phasing slope/offset, Prephasing slope/offset	The best-fit slope and offset of the phasing/prephasing corrections, calculated from the entire read.