Due to the complexity of these experiments and the data they generate, we have recommended ranges for some metrics, but most metrics are very sample-specific. If you have any questions about any metrics on your report, please contact Support (email@example.com).
- # cells: For V2 chemistry, expected cell throughput is from 2-10k cells, often less for nuclei. For V3 chemistry, the expected cell throughput is between 5-30k cells, with a median of 11k.
- Mean reads/cell/amplicon: This is the average number of reads covering each amplicon in each cell (i.e., the mean read depth per amplicon in each cell). We recommend that this number be between 35 and 150. Going above this number may lead to an overrepresentation of false positives, while numbers below this can lead to missing information for rare events.
- Panel uniformity: This is the number of amplicons that have mean reads to the amplicon above 0.2 * the mean reads per amplicon per cell. This indicates whether high- or low-performing amplicons are present in your panel.
- % reads mapped to target: This indicates the percentage of your DNA library that mapped back to the specific targets of your panel.
- Read quality (Q30): This is the percentage of bases (in both R1 and R2 reads) that have a sequencing quality higher than 30. We recommend this be >= 85%
- % reads mapped to genome: This indicates the percentage of your DNA library that maps back to your reference genome. When this number is lower, that can indicate a high presence of primer dimers in your library.