UhBRC5

3,518
Number of Spots Under Tissue
26,937
Mean Reads per Spot
1,590
Median Genes per Spot

Sequencing

Number of Reads
Total number of read pairs that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
Valid UMIs
Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.
Sequencing Saturation
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).
Q30 Bases in Barcode
Fraction of spot barcode bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Q30 Bases in RNA Read
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.
Q30 Bases in UMI
Fraction of UMI bases with Q-score >= 30, excluding very low quality/no-call (Q <= 2) bases from the denominator.
Number of Reads94,762,855
Valid Barcodes96.6%
Valid UMIs100.0%
Sequencing Saturation74.7%
Q30 Bases in Barcode98.0%
Q30 Bases in RNA Read91.6%
Q30 Bases in UMI97.2%

Mapping

Reads Mapped to Genome
Fraction of reads that mapped to the genome.
Reads Mapped Confidently to 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.
Reads Mapped Confidently to Intergenic Regions
Fraction of reads that mapped uniquely to an intergenic region of the genome.
Reads Mapped Confidently to Intronic Regions
Fraction of reads that mapped uniquely to an intronic region of the genome.
Reads Mapped Confidently to Exonic Regions
Fraction of reads that mapped uniquely to an exonic region of the genome.
Reads Mapped Confidently to Transcriptome
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.
Reads Mapped Antisense to Gene
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.
Reads Mapped to Genome76.8%
Reads Mapped Confidently to Genome73.9%
Reads Mapped Confidently to Intergenic Regions1.2%
Reads Mapped Confidently to Intronic Regions1.3%
Reads Mapped Confidently to Exonic Regions71.3%
Reads Mapped Confidently to Transcriptome69.3%
Reads Mapped Antisense to Gene1.3%
 

Spots

Fraction Reads in Spots Under Tissue
Of the reads that are confidently mapped to the transciptome, this is the fraction that have barcodes from spots covered by tissue.
Mean Reads per Spot
The total number of sequenced reads divided by the number of barcodes associated with a spot under tissue.
Median Genes per 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.
Total Genes Detected
The number of genes with at least one UMI count in any tissue covered spot.
Median UMI Counts per Spot
The median number of UMI counts per tissue covered spot.
Detected issue Image
Fraction Reads in Spots Under Tissue91.5%
Mean Reads per Spot26,937
Median Genes per Spot1,590
Total Genes Detected21,314
Median UMI Counts per Spot3,162

Sample

Sample IDUhBRC5
Sample Description
ChemistrySpatial 3' v1
Slide Serial NumberV10L27-275-D1
Reference Path
‎/gpfs/data/yanailab/projects/raoa04/10X/spaceGenome/refdata-gex-GRCh38-2020-A‎
TranscriptomeGRCh38-2020-A
Pipeline Versionspaceranger-1.1.0