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)