KCL_230

3,043
Number of Spots Under Tissue
42,313
Mean Reads per Spot
3,292
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 Reads128,757,704
Valid Barcodes97.9%
Valid UMIs100.0%
Sequencing Saturation61.8%
Q30 Bases in Barcode96.3%
Q30 Bases in RNA Read87.9%
Q30 Bases in UMI95.4%

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 Genome86.9%
Reads Mapped Confidently to Genome82.6%
Reads Mapped Confidently to Intergenic Regions1.5%
Reads Mapped Confidently to Intronic Regions1.3%
Reads Mapped Confidently to Exonic Regions79.9%
Reads Mapped Confidently to Transcriptome78.3%
Reads Mapped Antisense to Gene1.0%
 

Spots

Fraction Reads in Spots Under Tissue
The fraction of valid-barcode, confidently-mapped-to-transcriptome reads with tissue-associated barcodes.
Mean Reads per Spot
The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue.
Mean Reads Under Tissue per Spot
The number of reads under tissue 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 Tissue83.2%
Mean Reads per Spot42,313
Mean Reads Under Tissue per Spot34,528
Median Genes per Spot3,292
Total Genes Detected19,840
Median UMI Counts per Spot8,576

Sample

Sample IDKCL_230
Sample Description
ChemistrySpatial 3' v1
Slide Serial NumberV12U06-385-C1
Reference Path
‎/gpfs/data/yanailab/projects/lp2700/data_raw/references/refdata-gex-mm10-2020-A‎
Transcriptomemm10-2020-A
Pipeline Versionspaceranger-1.2.1