Sample information : Carassius_gibelio

Estimated number of cells: The total number of barcodes identified as cells.
Median UMI counts per cell: Among barcodes identified as cells, the median number of UMI per cell.
Median genes per cell: The median number of genes per cell.
Mean reads per cell: The mean number of reads per cell.

121 Estimated number of cell

9,380

Median UMI counts per cell

2,096

Median genes per cell

30,311

Mean reads per cell

Beads to cells

(left) Beads to cells plot: In library, different mRNAs from the same cell will carry the same cell barcode and random unique molecular identifiers (UMIs). However, some mRNA from dead cells mixed in reflection system was inevitability. This graph shows the distribution of UMI counts in each barcode. Barcodes can be determined to be cell-associated based on their UMI counts or by their expression profiles. Therefore, the graph contains both cell-associated (Colored Regions) and background-associated barcodes (Gray Regions).
(right) Histogram: Histograms of number of beads per droplet.

Summary

Estimated number of cells: The total number of barcodes identified as cells.
Mean reads per cell: The mean number of reads detected per cell.
Mean UMI counts per cell: The average number of UMI counts per cell. This item refers the average abundance of expression in each cell.
Median UMI counts per cell: The median number of UMI counts per cell.
Total genes detected: The total number of genes detected.
Mean genes per cell: The mean number of genes detected per cell. This item refers the activity of gene expression in each cell.
Median genes per cell: The median number of genes detected per cell.
Sequencing saturation: The fraction of UMI originating from an already-observed UMI.
Fraction reads in cells: The fraction of uniquely-mapped-to-transcriptome reads with cell-associated barcode.
Plot: The distribution of nFeature and nCount in violin.

Sample name

Carassius_gibelio

Species

Carassius_gibelio

Estimated number of cells

121

Mean reads per cell

30,311

Mean UMI count per cell

15,373

Median UMI counts per cell

9,380

Total genes detected

23,940

Mean genes per cell

2,568

Median genes per cell

2,096

Fraction reads in cells

98.37%

Sequencing saturation

41.16%

Sequencing

Number of reads: Number of raw off-machine reads obtained by this sequencing program.
Reads pass QC: Number of reads after quality control (QC) that can be used for downstream analysis. QC includes filtering low quality reads and invalid barcodes.
Reads with exactly matched barcodes: Number of reads with barcodes that match the barcode whitelist before correction.
Reads with failed barcodes: Number of reads with invalid barcodes that fail to match the barcode whitelist.
Reads filtered on low quality: Number of reads in low quality. The QC will filter the average base quality < Q20 or 2 bases < Q10 in the first 15 bases.
Q30 bases in cell barcode: Fraction of cell barcode bases with Q-score ≥ 30.
Q30 bases in UMI: Fraction of UMI bases with Q-score ≥ 30.
Q30 bases in reads: Fraction of RNA read bases with Q-score ≥ 30.

mRNA

Number of reads

6,967,703

Reads pass QC

95.94%

Reads with exactly matched barcodes

100.0%

Reads with failed barcodes

0.0%

Reads filtered on low quality

0.0%

Q30 bases in cell barcode

87.79%

Q30 bases in UMI

87.78%

Q30 bases in reads

94.16%

Droplet index

Number of reads

218,724,924

Reads pass QC

96.18%

Reads with exactly matched barcodes

90.21%

Reads with failed barcodes

3.26%

Reads filtered on low quality

0.56%

Q30 bases in cell barcode

95.89%

Q30 bases in reads

96.75%

Mapping & Annotation

Reads pass QC: Number of reads after quality control (QC) that can be used for downstream analysis. QC includes filtering low quality reads and invalid barcodes.
Reads mapped to genome: Fraction of reads that mapped to the genome.
Plus strand: The number of reads in plus strand.
Minus strand: The number of reads in minus strand.
Mitochondria ratio: The fraction of reads mapped to mitochondria.
Mapping quality corrected reads: The number of reads that align to a single exonic locus but also align to 1 or more non-exonic loci.
Reads mapped to exonic regionse: Fraction of reads that mapped to an exonic region of genome.
Reads mapped to intronic regions: Fraction of reads that mapped to an intronic region of genome.
Reads mapped antisense to gene: Fraction of reads mapped to transcriptome, but on the opposite strand of their annotated gene. This part of reads will be filtered out cause them are opposite to theoretical direction.
Reads mapped to intergenic regions: Fraction of reads that mapped to intergenic regions of genome.

Reads pass QC

6,684,656

Reads mapped to genome

55.89%

Plus strand

58.43%

Minus strand

41.57%

Mitochondria ratio

0.00%

Mapping quality corrected reads

0.79%

Reads mapped to exonic regions

90.0%

Reads mapped to intronic regions

3.5%

Reads mapped antisense to gene

3.3%

Reads mapped to intergenic regions

6.5%

Include introns

True

Cluster

Left: The figure is automated clustering each cell-barcode by UMAP algorithm. The cells clustered into the same group have similar expression profiles. Each dot represents a cell, and is colored according to different cluster.
Right: This plot shows that the total UMI counts for each cell-barcode. Two-dimensional horizontal and vertical coordinates of each dot are obtained using the uniform manifold approximation and projection (UMAP) algorithm. Each dot represents a cell and is colored according to UMI counts. Cells with greater UMI counts likely have higher RNA content than cells with fewer ones.

Marker

Table: The table shows the top 30 differentially expressed genes for each cluster. Here a differential expression test was performed between each cluster and the rest of the sample for each gene. The p-value is a measure of the statistical significance of the expression difference, the smaller the P value, the closer to the theoretical value. Avg_log2FC is log fold-chage of the average expression between the markers for every cluster compared to all remaining cells.

Select:

gene	cluster	p_val_adj	p_val	avg_log2FC	pct.1	pct.2
LOC127954054	0	0.07371816891984119	0.00019770047918063114	4.846	0.52	0.061
fosab	0	0.003037239778017313	1.9866822200531876e-06	3.646	0.72	0.152
LOC127937979	0	0.0024941719166783143	8.157286488351367e-07	3.502	0.76	0.182
fosb	0	0.005879689640843961	6.538116424277036e-06	3.287	0.7	0.121
LOC127952357	0	0.0012420351488550937	3.249699499882506e-07	2.858	0.86	0.273
LOC128027522	0	0.004689674767822308	4.294573963207242e-06	2.787	0.96	0.788
LOC128013826	0	0.006297682949491352	9.062599744165996e-06	2.763	0.76	0.273
ppp1r15a	0	0.052111925142116364	0.00011930385792609058	2.569	0.66	0.182
LOC127963554	0	0.06005418729826495	0.00014141488374787663	2.079	0.74	0.333
LOC127948379	0	0.06417326752326351	0.00015531206818162938	1.782	0.9	0.606
LOC127935236	0	0.09460089048254842	0.00028464422829652195	1.69	0.84	0.485
LOC127966684	0	0.08643736834576135	0.00023746529765319052	1.667	0.8	0.485
LOC128030969	0	0.0004244353693136694	2.7762648437576495e-08	1.573	1.0	1.0
LOC127957133	0	0.0033174396538316418	2.3869594578851426e-06	1.545	0.98	0.758
LOC127953702	0	0.07282374569869011	0.0001905383194628208	1.516	0.92	0.788
LOC127979345	0	0.03808419903844602	7.971574890307907e-05	1.491	0.96	0.788
atp5if1a	0	0.09460089048254842	0.00028464422829652195	1.256	0.9	0.758
LOC128015180	0	0.037813785020832796	7.667630400613663e-05	1.205	0.96	0.818
LOC127974318	0	0.006297682949491352	8.310709724205002e-06	1.178	1.0	1.0
LOC127934901	0	0.009281255550589609	1.5455169774513712e-05	1.131	0.94	0.909
LOC127945119	0	0.01815635600016943	3.3253399267709574e-05	0.855	1.0	0.97
LOC127978747	0	0.06858976135055113	0.0001704873712271679	0.638	0.96	0.97
col10a1a	1	0.003994864487256814	3.135686410719634e-06	3.361	0.758	0.26
LOC128031526	1	0.003037239778017313	1.8538947883984573e-06	3.062	0.909	0.34
LOC128013379	1	0.01979657533579683	3.7552373413010733e-05	2.312	0.788	0.4
ND2	1	0.002499796693544307	1.2482385933728384e-06	2.172	1.0	0.82
ND4	1	0.0012420351488550937	2.9444554040483666e-07	2.152	1.0	0.86
LOC127946536	1	0.002499796693544307	1.009925780042992e-06	2.11	0.97	0.78
LOC127944517	1	0.004689674767822308	4.294573963207242e-06	2.086	1.0	0.9
LOC127968066	1	0.0009124778562736837	1.1937177606929404e-07	2.039	1.0	0.86
timp2b	1	0.006297682949491352	8.678876605412332e-06	1.965	0.939	0.7
ND1	1	0.00885727047698688	1.3904663229178775e-05	1.901	1.0	0.94
LOC127979389	1	0.013015995279269303	2.2987432793058033e-05	1.834	0.939	0.72
ND3	1	0.0046897026857855425	4.908113747551588e-06	1.822	1.0	0.8
LOC127943055	1	0.07197925608237264	0.00018362055123054245	1.8	0.758	0.42
COX3	1	0.002499796693544307	1.308109206459606e-06	1.797	1.0	0.98
unassigned_gene_4	1	0.006297682949491352	8.678876605412332e-06	1.753	1.0	1.0
COX1	1	0.0046897026857855425	4.69482373316876e-06	1.741	1.0	0.98
ATP6	1	0.006426756756315887	9.668720918057653e-06	1.718	0.97	0.98
col1a1a	1	0.009281255550589609	1.578444821528845e-05	1.716	0.909	0.8
col1a2	1	0.08755763107305334	0.0002462701554252547	1.624	0.879	0.74
CYTB	1	0.02636878384870072	5.174408133575494e-05	1.614	1.0	0.98
COX2	1	0.006297682949491352	8.678876605412332e-06	1.607	1.0	1.0
unassigned_gene_2	1	0.044798003436450524	9.66989870096067e-05	1.563	1.0	1.0
LOC128018199	1	0.052111925142116364	0.00011705913475237817	0.912	1.0	1.0
LOC127975281	1	0.08873313251973335	0.0002553805488532357	0.866	1.0	0.96

Saturation

Left: The plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. Sequencing Saturation is a measure of the observed library complexity, and approaches 1.0 (100%) when all converted mRNA transcripts have been sequenced. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.
Right: The plot shows the Median Genes per Cell as a function of downsampled sequencing depth in mean reads per cell, up to the observed sequencing depth. The slope of the curve near the endpoint can be interpreted as an upper bound to the benefit to be gained from increasing the sequencing depth beyond this point.