V1_Adult_Mouse_Brain - Adult Mouse Brain (Coronal) - Using Space Ranger 2.1

Total number of read pairs that were assigned to this library in demultiplexing.

Fraction of reads with barcodes that match the whitelist after barcode correction.

Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.

The 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 spot-barcode, valid UMI reads that had a non-unique spot-barcode/UMI/gene combination.

Fraction of spot barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.

Fraction of RNA read bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator. This is Read 2 for the Visium v1 chemistry.

Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.

Fraction of reads that mapped to the genome.

Fraction 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.

Fraction of reads that mapped uniquely to an intergenic region of the genome.

Fraction of reads that mapped uniquely to an intronic region of the genome.

Fraction of reads that mapped uniquely to an exonic region of the genome.

Fraction 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.

Fraction 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.

Shows the tissue image in gray tones with an overlay of the aligned fiducial frame (open blue circles) and the capture area spots (gray circles). For the latter, the circles filled in red denote selected tissue-associated spots and the remaining open gray circles denote unselected spots. Hover mouse cursor over the image to magnify the view. Confirm fiducial frame aligns well with fiducial spots, e.g. the corner shapes match, and confirm selection of tissue-covered spots. If the result shows poor fiducial alignment or tissue detection, consider sharing the image with support@10xgenomics.com so we can improve the algorithm. Otherwise, perform manual alignment and spot selection with Loupe Browser.

The fraction of valid-barcode, confidently-mapped reads with tissue-associated barcodes.

The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.

The number of reads under tissue divided by the number of barcodes associated with a spot under tissue.

The median number of UMI counts per tissue covered spot.

The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count.

The number of genes with at least one UMI count in any tissue covered spot.