Number of ReadsTotal number of read pairs that were assigned to this library in demultiplexing.Number of Short Reads SkippedTotal number of read pairs that were ignored by the pipeline because they do no satisfy the minimum length requirements (for example read1 less that 26 bases in 3' v2 or 3' v3 or 5').Valid BarcodesFraction of reads with barcodes that match the whitelist after barcode correction.Valid UMIsFraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.Sequencing SaturationThe fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene). This metric was called 'cDNA PCR Duplication' in versions of Cell Ranger prior to 1.2.Q30 Bases in BarcodeFraction of cell barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.Q30 Bases in RNA ReadFraction of RNA read bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 1 for the Single Cell 3' v1 chemistry and Single Cell 5' paired end, Read 2 for the Single Cell 3' v2/v3 chemistry and Single Cell 5' R2-only).Q30 Bases in RNA Read 2Fraction of RNA read 2 bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.Q30 Bases in UMIFraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.| Number of Reads | 5,945,636 |
| Number of Short Reads Skipped | 0 |
| Valid Barcodes | 94.7% |
| Valid UMIs | 100.0% |
| Sequencing Saturation | 9.3% |
| Q30 Bases in Barcode | 93.6% |
| Q30 Bases in RNA Read | 86.6% |
| Q30 Bases in RNA Read 2 | 83.9% |
| Q30 Bases in UMI | 93.4% |
Reads Mapped to GenomeFraction of reads that mapped to the genome.Reads Mapped Confidently to GenomeFraction of reads that mapped uniquely to the genome. If a gene mapped to exonic loci from a single gene and also to non-exonic loci, it is considered uniquely mapped to one of the exonic loci.Reads Mapped Confidently to Intergenic RegionsFraction of reads that mapped uniquely to an intergenic region of the genome.Reads Mapped Confidently to Intronic RegionsFraction of reads that mapped uniquely to an intronic region of the genome.Reads Mapped Confidently to Exonic RegionsFraction of reads that mapped uniquely to an exonic region of the genome.Reads Mapped Confidently to TranscriptomeFraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting.Reads Mapped Antisense to GeneFraction of reads confidently mapped to the transcriptome, but on the opposite strand of their annotated gene. A read is counted as antisense if it has any alignments that are consistent with an exon of a transcript but antisense to it, and has no sense alignments.| Reads Mapped to Genome | 82.6% |
| Reads Mapped Confidently to Genome | 78.0% |
| Reads Mapped Confidently to Intergenic Regions | 5.8% |
| Reads Mapped Confidently to Intronic Regions | 5.7% |
| Reads Mapped Confidently to Exonic Regions | 66.6% |
| Reads Mapped Confidently to Transcriptome | 68.8% |
| Reads Mapped Antisense to Gene | 2.5% |