Sequencing Metrics and Charts
ElemBio Cloud displays initial estimates for metrics and charts that AVITI OS generates. The following sections describe the metrics and charts available in ElemBio Cloud. Available charts and metrics depend on the run setup and the version of AVITI OS that the run uses. To compute final metrics for a run, execute Bases2Fastq.
Sequencing Run Metrics
PhiX-related metrics only apply to library pools that include a spike-in of PhiX Control Library. The Q50 metric is only available for runs that use Cloudbreak UltraQ chemistry. For more information about Indexing Assignment metrics, see Indexing Assignment.
| Metric | AVITI OS Version | Description | Value |
|---|---|---|---|
| Avg Q Score | AVITI OS v2.2.0+ | The median Q score for the base calls in a cycle | Numeric characters |
| Indexing Assignment, Perfect Match | AVITI OS v2.0.0+ | The percentage of reads with indexes assigned that have a perfect index match | Percentage |
| Indexing Assignment, Partial Match | AVITI OS v2.0.0+ | The percentage of reads with indexes assigned that have a partial index match | Percentage |
| PF | AVITI OS v1.0.0+ | The percentage of reads in the library pool that pass the quality filter process | Percentage |
| % PhiX Aligned | AVITI OS v2.2.0+ | The percentage of reads in Read 1 and Read 2 that align to the PhiX Control Library | Percentage |
| PhiX Error Rate | AVITI OS v1.0.0+ | The percentage of control reads per cycle that do not align to PhiX Control Library | Percentage |
| Q30 | AVITI 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 rate | Percentage |
| Q40 | AVITI 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 rate | Percentage |
| Q50 | AVITI OS v2.6.0+ | The percentage of base calls ≥ Q50, which indicates an incorrect base probability of 1 in 100,000 or a 99.999% confidence rate | Percentage |
| Reads1 | AVITI OS v1.0.0+ | The number of reads the library pool generates | Value in billions (B) |
| Yield1 | AVITI OS v1.0.0+ | The amount of sequencing data generated or projected | Value in gigabases (Gb) |
1 The cycle when Reads and Yield first appear depends on the library prep workflow.
Sequencing 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.
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.
| Chart | AVITI OS Version | Description |
|---|---|---|
| Q Scores |
| The percentage of base calls with a Q score ≥ Q30, a Q score ≥ Q40, a Q score ≥ Q50, and the average Q score for each cycle in Read 1 and Read 2. The chart for Q50 only appears when a run uses Cloudbreak UltraQ chemistry. |
| PhiX Error Rate |
| 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 |
| 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 Composition | AVITI 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 Thumbnail | AVITI 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.
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.
If you have a library with a low diversity of base composition in the first five cycles of Read 1, contact Element Technical Support.