Summary-Protein

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 Protein Expression Distribution
Spatial protein expression distribution plot shows MID count at each spot (bin20)
All Bins
Bins under Tissue
Plot with Spot Colored by MID Count
1,307,126,096
Total Reads
1,064,911,668
Valid CID Reads
970,550,859
Valid PID Reads
231,664,295
Unique PID Reads
Key Metrics

###### Total Reads

Total number of sequenced reads

###### Valid CID Reads

Number of reads with CIDs matching the mask file and with MIDs passing QC

###### Invalid CID Reads

Number of reads with CIDs that cannot be matched with the mask file

###### Valid PID Reads

Valid CID reads that mapped to the protein sequence in the protein sequence database

###### Invalid PID Reads

Valid CID reads that can not be mapped to the protein sequence in the protein sequence database

###### Unique PID Reads

Total number of unique protein reads (PID reads whose MIDs are different)

###### Sequencing Saturation

Number of PID reads with duplicated MID
Total Reads
100%
1,307,126,096
Valid CID Reads
81.5%
1,064,911,668
Valid PID Reads
91.1%
970,550,859
Unique PID Reads
23.9%
231,664,295
Sequencing Saturation
76.1%
738,886,564
Invalid PID Reads
8.9%
94,360,809
Invalid CID Reads
18.5%
242,214,428
Sequencing

###### Rate of Q30 Bases in CID

Ratio of CID (Coordinate ID) bases with quality value exceeded 30

###### Rate of Q30 Bases in MID

Ratio of MID (Molecule ID) bases with quality value exceeded 30

###### Rate of Q30 Bases in PID

Ratio of PID (Protein ID) bases with quality value exceeded 30

###### Rate of Valid PID Reads in Total

Valid PID reads / total reads, ratio of valid PID reads over total reads
Rate of Q30 Bases in CID
88.19%
Rate of Q30 Bases in MID
88.26%
Rate of Q30 Bases in PID
94.85%
Rate of Valid PID Reads in Total
74.25%
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 MID (MID Under Tissue / Total MID)
Tissue Area
12.1
Number of MID Under Tissue Coverage
149,011,206
Fraction MID in Spots Under Tissue
64.37%
Tissue Segmentation
Sequencing Saturation
(left) 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)
Protein Correlations
Spearman correlation between raw antibody counts under tissue, except isotype. Antibodies are clustered based on Spearman correlation coefficient (in bin50).
Histogram of Protein Counts
Distribution of spot numbers vs log-scaled MID count (in bin50).
Information
Species
mouse
Tissue
thymus
Reference
mouse
FASTQ
E100079141_L01_4_1,E150023160_L01_11_1
Command Line
saw realign --id=A02677B5_DAPI_Demo_Realign --sn=A02677B5 --count-data=./A02677B5 --realigned-image-tar=./A02677B5_SC_20241119_211910_4.1.0.tar.gz