Summary-Gene

Analytical Report
A02677B5_DAPI_Demo_Realign
Alerts
Metrics
Value
Alert
Note

- Summary
Gene Protein
- Square Bin
  Gene Protein
- Cell Bin
  Gene Protein
- Image
- Analysis

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
1,346,328,616
Total Reads
7,497
Mean MID per Bin50
2,395
Mean Gene per Bin50
28,374
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%
1,346,328,616
Valid CID Reads
80.5%
1,083,603,687
Clean Reads
74.5%
806,755,913
Uniquely Mapped Reads
71.8%
579,636,231
Transcriptome
76.0%
440,757,801
Unique Reads
46.9%
206,873,753
Sequencing Saturation
53.1%
233,884,048
Unannotated Reads
24.0%
138,878,430
Multi-Mapped Reads
13.0%
105,236,518
Unmapped Reads
15.1%
121,883,164
Non-Relevant Short Reads
22.7%
246,464,946
Discarded MID Reads
2.8%
30,382,828
Invalid CID Reads
19.5%
262,724,929
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
91.67%
CID Q30
89.85%
MID Q30
85.73%
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
333,297,600
Intronic
107,460,201
Intergenic
94,758,451
Antisense
44,119,979
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
12.1
Number of MID Under Tissue Coverage
149,067,432
Fraction MID in Spots Under Tissue
72.06%
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
Species
mouse
Tissue
thymus
Reference
mouse
FASTQ
V350248064_L01_read_1,V350248064_L02_read_1,V350248064_L03_read_1,V350248064_L04_read_1
Command Line
saw realign --id=A02677B5_DAPI_Demo_Realign --sn=A02677B5 --count-data=./A02677B5 --realigned-image-tar=./A02677B5/A02677B5_SC_20241119_211910_4.1.0.tar.gz