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Metrics and Charts

Run Metrics

The following table lists metrics available in ElemBio Cloud. Available metrics depend on run setup and the version of AVITI Operating Software (AVITI OS).

PhiX-related metrics only apply to library pools that include a spike-in of PhiX Control Library. For more information about Indexing Assignment metrics, see Indexing Assignment.

MetricAVITI OS VersionDescriptionValue
Avg Q ScoreAVITI OS v2.2.0+The median Q-score for the base calls in a cycleNumeric characters
Indexing Assignment, Perfect MatchAVITI OS v2.0.0+The percentage of reads with indexes assigned that have a perfect index matchPercentage
Indexing Assignment, Partial MatchAVITI OS v2.0.0+The percentage of reads with indexes assigned that have a partial index matchPercentage
PFAVITI OS v1.0.0+The percentage of reads in the library pool that pass the quality filter processPercentage
% PhiX AlignedAVITI OS v2.2.0+The percentage of reads in Read 1 and Read 2 that align to the PhiX Control LibraryPercentage
PhiX Error RateAVITI OS v1.0.0+The percentage of control reads that do not align to PhiX Control LibraryPercentage
Q30AVITI OS v1.0.0+The percentage of base calls ≥ Q30, which indicates an incorrect base probability of 1 in 1000 or a 99.9% confidence ratePercentage
Q40AVITI OS v2.2.0+The percentage of base calls ≥ Q40, which indicates an incorrect base probability of 1 in 10,000 or a 99.99% confidence ratePercentage
Reads1AVITI OS v1.0.0+The number of reads the library pool generatesValue in billions (B)
Yield1AVITI OS v1.0.0+The amount of sequencing data generated or projectedValue in gigabases (Gb)

1 The cycle when Reads and Yield first appear depends on the library prep workflow.

Run Charts

Run charts are available on the Primary Analysis tab of a Run Details page and graph quality metrics as they appear throughout the run. Available charts depend on run setup and the version of AVITI Operating Software (AVITI OS).

For each chart, you can expand the view or export the chart as an image. If you are using the individually addressable lanes add-on, you can view information for Library Pool 1 and Library Pool 2.

ChartAVITI OS VersionDescription
Q-Scores
  • AVITI OS v1.0.0+ for Q30
  • AVITI OS v2.2.0+ for Q40 and average Q-score
The percentage of base calls with a Q-score ≥ Q30, a Q-score ≥ Q40, and the average Q-score for each cycle in Read 1 and Read 2.
PhiX Error Rate
  • AVITI OS v1.0.0+ for PhiX error rate
  • AVITI OS v2.2.0+ for % PhiX Aligned
The percentage of control reads that do not align to a spike-in of PhiX Control Library. The chart only appears when the library pool includes a spike-in of PhiX Control Library.
Indexing Assignment
  • AVITI OS v2.0.0+ for indexing assignment
  • AVITI OS v2.4.0+ for top unassigned sequences
The percentages of reads assigned with a perfect index match or an index mismatch. Expand the chart to view tables that list the top samples with a mismatch, unassigned sequences, and samples with low representation. See Indexing Assignment.
Base CompositionAVITI OS v2.2.0+The percentage of adenine (A), cytosine (C), guanine (G), and thymine (T) bases in each cycle of Read 1, Read 2, Index 1, and Index 2. See Base Composition.
Image ThumbnailAVITI OS v2.2.0+A snapshot of the polonies on a tile from the first cycle of Read 1. The image indicates sample density and loading concentration on the flow cell, providing a quality check to identify overloading or underloading.

Indexing Assignment

Indexing assignment charts and metrics show estimated index quality, which can help identify potential problems with the run manifest or library. The indexing assignment metrics and charts in ElemBio Cloud and AVITI OS are only available for runs that meet the following requirements:

  • For runs with dual-indexed libraries, the run manifest must include 1–768 index pairs across both lanes.
  • For runs with single-indexed libraries, the run manifest must include 1–768 index sequences across both lanes.
NOTE

Using Bases2Fastq, you can successfully demultiplex more than 768 index pairs or sequences. The limitation only applies to the metrics and charts that the ElemBio Cloud and AVITI OS interfaces display.

Base Composition

Base composition data help confirm the accuracy of your run. By reviewing the percentage of bases for different cycles, you can also identify potential causes for changes in run quality. For example, an unexpected change in the Q30 metric can correlate to a change in the base composition for a cycle.