illumina MiSeq System Manual page 38

MiSeq System Guide
Q-Score Probability of Wrong Base Call
Q20 1 in 100
Q10 1 in 10
Cluster Density (K/mm²)—Shows the number of clusters per square millimeter for the run.
u
Clusters Passing Filter (%)—Shows the percentage of clusters passing filter based on the Illumina
u
chastity filter, which measures quality. This data appears only after cycle 25.
NOTE
The chastity of a base call is the ratio of the intensity of the greatest signal divided by the sum of the 2
greatest signals. If more than 1 base call has a chastity value of less than 0.6 in the first 25 cycles, reads
do not pass the quality filter.
Estimated Yield (Mb)—Shows the projected number of bases called for the run, measured in
u
megabases. This data appears only after cycle 25.
2 When the run is complete, the Next button appears. Review the results on the Sequencing screen before
proceeding.
NOTE
The Sequencing screen remains viewable until Next is selected. After you select Next, it is not possible to
return to the Sequencing screen.
3 Select Next to exit the Sequencing screen and proceed to a post-run wash.
Template Generation
Template generation is the process where cluster positions over the entire flow cell surface are defined
according to X and Y coordinate position. Real-time analysis (RTA) uses early cycles of the run for template
generation.
After the template of cluster positions is generated, images produced over every subsequent cycle of imaging
are aligned against the template. Individual cluster intensities in all four nucleotide color channels are
extracted and base calls are produced from the normalized cluster intensities.
Run Metrics
Run metrics appear on the Sequencing screen at different points in a run. During cluster generation steps, no
metrics appear.
After sequencing begins, the following metrics appear at the indicated cycles:
Metric
Intensity
Intensity and Cluster Density
Intensity, Cluster Density, % PF,
Yield, and Q-scores
Document # 15027617 v04 Material # 20024228
For Research Use Only. Not for use in diagnostic procedures.
Kit
MiSeq Reagent Kits, v3
MiSeq Reagent Kits, v2
MiSeq Reagent Kits, v1
MiSeq Reagent Kits, v3
MiSeq Reagent Kits, v2
MiSeq Reagent Kits, v1
MiSeq Reagent Kits, v3
MiSeq Reagent Kits, v2
MiSeq Reagent Kits, v1
Cycle
Cycle 1–7
Cycle 1–4
Cycle 1–4
Cycle 8–25
Cycle 5–25
Cycle 5–25
Cycle 26 through run completion
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