Analytical Report
D04701A4
  • Summary
  • Square Bin
  • Cell Bin
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Spatial Gene Expression Distribution
Spatial Gene expression distribution plot shows MID count at each spot (bin20)
All Bins
Bins under Tissue
Plot with Spot Colored by MID Count
3,191,005,215
Total Reads
1,444
Mean MID per Bin50
363
Mean Gene per Bin50
43,951
Total Genes
Key Metrics
Total Reads
Total number of sequenced reads
Valid CID Reads
Number of reads with CIDs that can be matched with the mask file
Clean Reads
Number of Valid CID Reads that have passed QC
Uniquely Mapped Reads
Number of reads that mapped uniquely to the reference genome. If the pipeline uses uniquely mapped reads and the best match from multi-mapped reads for subsequent annotation, this item will include them both
Transcriptome
Number of reads that are aligned to transcripts of at least one gene
Unique Reads
Number of reads in Transcriptome that have been corrected by MAPQ and deduplicated
Sequencing Saturation
Number of reads in Transcriptome that have been corrected by MAPQ with duplicated MID
Unannotated Reads
Number of reads that cannot be aligned to the transcript of one gene
Multi-Mapped Reads
Number of reads that mapped more than one time on the genome
Unmapped Reads
Number of reads that cannot be mapped to the reference genome
Non-Relevant Short Reads
Number of non-relevant short reads
Discarded MID Reads
Number of reads with MID that have been discarded since MID sequence quality does not satisfy with further analysis
Invalid CID Reads
Number of reads with CIDs that cannot be matched with the mask file
Total Reads
100%
3,191,005,215
Valid CID Reads
40.5%
1,293,462,171
Clean Reads
87.5%
1,132,337,284
Uniquely Mapped Reads
77.4%
876,034,494
Transcriptome
81.6%
714,470,056
Unique Reads
26.5%
189,501,524
Sequencing Saturation
73.5%
524,968,532
Unannotated Reads
18.4%
161,564,438
Multi-Mapped Reads
9.5%
107,669,384
Unmapped Reads
13.1%
148,633,406
Non-Relevant Short Reads
9.2%
118,637,549
Discarded MID Reads
3.3%
42,487,338
Invalid CID Reads
59.5%
1,897,543,044
Sequencing
Total Q30
Ratio of bases with quality value exceeded 30 in the sequenced reads
CID Q30
Ratio of CID (Coordinate ID) bases with quality value exceeded 30
MID Q30
Ratio of MID (Molecule ID) bases with quality value exceeded 30
Total Q30
95.3%
CID Q30
79.82%
MID Q30
92.58%
Annotation
Exonic
Number of reads that mapped uniquely to an exonic region and on the same strand of the genome
Intronic
Number of reads that mapped uniquely to an intronic region and on the same strand of the genome
Intergenic
Number of reads that mapped uniquely to an intergenic region and on the same strand of the genome
Antisense
Number of reads mapped to the transcriptome but on the opposite strand of their annotated gene
Exonic
402,250,280
Intronic
312,219,776
Intergenic
85,608,110
Antisense
74,456,687
Tissue Segmentation
Tissue
Tissue Area
Tissue area in mm²​
Number of MID Under Tissue Coverage
Number of MID under tissue coverage
Fraction MID in Spots Under Tissue
Fraction of MID under tissue over total unique reads (MID Under Tissue / Unique Reads)
Tissue Area
41.69
Number of MID Under Tissue Coverage
99,932,496
Fraction MID in Spots Under Tissue
52.73%
Sequencing Saturation
(left) Plot of the median number of genes detected per bin as a function of sequencing depth(bin50)
(middle) Plot of the unique reads detected per bin as a function of sequencing depth(bin50)
(right) Plot of the sequencing saturation as a function of sequencing depth(bin50)
Information
Command Line
saw count --id=D04701A4 --sn=D04701A4 --omics=transcriptomics '--kit-version=Stereo-seq N FFPE V1.0' --sequencing-type=PE75_25+59 --organism=mouse --tissue=embryo --chip-mask=/home/yhanda/script/RNAseq/STOmics/package/250422_FFPE_mouse/mask/D04701A4.barcodeToPos.h5 --fastqs=/home/yhanda/script/RNAseq/STOmics/package/250422_FFPE_mouse/reads --image-tar=/home/yhanda/script/RNAseq/STOmics/package/250422_FFPE_mouse_2nd/image/D04701A4_SC_20250424_094100_4.1.2.tar.gz --reference=/home/yhanda/script/RNAseq/STOmics/package/saw-8.1.1/transcriptome