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Sample information : Acomys_dimidiatus



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.
479

Estimated number of cell

9,913

Median UMI counts per cell

1,245

Median genes per cell

45,460

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
Acomys_dimidiatus
Species
Acomys_dimidiatus
Estimated number of cells
479
Mean reads per cell
45,460
Mean UMI count per cell
10,032
Median UMI counts per cell
9,913
Total genes detected
8,461
Mean genes per cell
1,250
Median genes per cell
1,245
Fraction reads in cells
99.36%
Sequencing saturation
39.44%
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
25,891,036
Reads pass QC
96.72%
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
87.51%
Q30 bases in UMI
87.66%
Q30 bases in reads
94.00%
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
25,041,950
Reads mapped to genome
87.83%
Plus strand
48.85%
Minus strand
51.15%
Mitochondria ratio
0.00%
Mapping quality corrected reads
0.85%
Reads mapped to exonic regions
42.6%
Reads mapped to intronic regions
0.7%
Reads mapped antisense to gene
1.1%
Reads mapped to intergenic regions
56.8%
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.
gene cluster p_val_adj p_val avg_log2FC pct.1 pct.2
g444000.060304665573197720.0055309012803820393.1460.1860.026
g934700.00284752921475193640.000161331906693785743.1180.2560.041
g44103.888984165688679e-087.593874406374342e-102.710.4490.107
g165600.0169387409218971080.00126038264551985872.7030.2440.063
g535900.00347197505643824420.00020390149369910992.6510.2630.044
g1199800.00157923687255490138.316691222330545e-052.6030.3010.085
g977200.034067697855506140.00284233455480850052.5790.2240.056
g1414300.00076666966855370023.629205531615149e-052.570.3080.078
g676600.0014255532616849537.317558902436076e-052.4950.3140.096
g970100.000220261941811528159.383940716230785e-062.4660.340.093
g114700.040737633548550190.00348921447109623632.4280.2180.048
g1107100.0135324130154275220.00095287405256560652.4050.250.059
g355200.058775310714659450.00537324586119223952.340.2120.052
g1322000.00097012091612513744.7788500749951294e-052.3250.3210.089
g246204.479701256842328e-124.903814985300773e-142.3020.6030.211
g653508.074961958812383e-062.5084940996310656e-072.2430.4420.167
g1109400.0251236561796522840.0019846201775050772.2360.2440.07
g650300.027894190277069250.00225711865111788162.2360.2440.07
g561000.0174391838539227870.0013079387890442092.2160.250.067
g305400.000281677906287578871.2375493811747177e-052.2040.3590.13
g79200.029423005312901390.00241237817464160132.2040.250.078
g1134901.1640562704470753e-082.152470914288231e-102.2030.5130.174
g1331100.057064076366404770.00519992175173155952.1450.2310.078
g615100.049170295160367370.004306037682683062.140.2310.07
g1358805.856719429586373e-182.5124979801480002e-202.1380.8330.53
g1131400.0022348645368473540.00012430607483056292.1360.3080.093
g869700.0153333061756568520.00110463315200368142.1320.2630.081
g167703.197511685517407e-217.568074995307473e-242.1040.8530.481
g627600.035160725328075470.00295433313407498072.0760.2370.067
g689200.066623110143922980.0062582359380756052.0750.2240.067
g791200.0002546563423829851.1037619573700385e-052.0690.3910.159
g433700.097432619493354740.0099045024469997832.0670.1990.048
g1222600.0048517413949697270.000300004127677122172.0630.2950.085
g791300.000226249435085485749.672498038417956e-062.0530.3850.137
g796200.0124748791675333220.00087287246246202082.0390.2760.089
g895000.000374429193131711871.6782846970252765e-052.0370.3650.141
g256400.042444014450915310.00364792491064819432.0320.2560.096
g1066000.0135631832427074610.00095704710159341112.0210.2630.078
g260401.086413026432364e-081.992828628367058e-102.0090.5450.23
g1135309.210135088879758e-062.9020100206085627e-072.0070.4290.141
g1279405.51684217241389e-081.1098972417874099e-091.9940.5580.274
g574300.0110824886550283560.00076560979318021321.9890.2880.1
g224300.061838681023188010.005735629142239481.9750.2440.089
g173206.4399101157936e-172.9532132187810885e-191.9680.8460.489
g1025600.00273222501378977360.00015358661320120031.9590.3330.137
g715601.426923474238454e-194.85491714607758e-221.9530.8780.611
g362709.481948384216592e-063.043761537536983e-071.9530.4490.174
g1272400.0097233158831721970.00065778417689865851.9530.2880.1
g173302.429687656959502e-151.6533377547357557e-171.9480.8140.515
g744700.00305854454054645160.000177359387558314961.9480.3270.119
g213710.06627347746204489.413157007571379e-050.2521.00.989
g765210.00173562046956492155.134971803446513e-070.2041.01.0
g691610.066694825612082550.000128259280023235670.191.01.0
g768610.0082258478675202913.6505242015622592e-060.1891.01.0
g1022510.0262739661371962.332008828745207e-050.1881.00.996
g208610.00173562046956492154.32628874582849e-070.1731.01.0
g714610.066462674876093360.000109032065266899220.1731.01.0
g1389910.06627347746204489.803768855332071e-050.1721.00.996
g913210.035474000315302953.673343227915986e-050.1641.01.0
g424010.066462674876093360.000117981079661704190.1591.01.0
g1185810.061563533654485647.285625284554514e-050.1461.01.0
g217610.0155807122622115799.219356368172532e-060.1441.01.0
g1055310.0262739661371962.1012620318157597e-050.121.01.0
g113525.9953240362725444e-051.9688786036279656e-060.8590.7520.621
g1366720.0241909808600266620.00185368758661151060.5280.7610.751
g1194620.0193506672313691550.00142553731970737270.4240.7950.777
g890923.6399369528247955e-051.1469032114669844e-060.4211.01.0
g714521.328964248158293e-053.55832143367827e-070.4030.9740.964
g1239729.826479384403893e-144.506225753202968e-160.4021.00.997
g1151325.5398488372353155e-142.458512797589637e-160.3871.01.0
g1229720.072080892910178860.0070801350432483370.3780.8120.816
g1174220.097193368321955520.0103375786721133160.3760.7610.786
g299120.00135687182707131786.342773629504977e-050.370.9910.977
g1324520.0280741284221617780.00223101804985438750.3580.8550.861
g1170520.016895504373687530.00119846986557484870.3540.9660.958
g1230920.0194893572971119070.00143863746912113040.3480.9230.922
g1346821.0223533015421683e-143.3271853008768786e-170.3431.01.0
g556420.00079021123982788443.49516509923872e-050.3421.00.981
g752523.763979512328157e-177.795223842099733e-200.331.01.0
g1019521.4654966710649e-111.0839472419119082e-130.3291.01.0
g68520.0023137570499963430.000115687852499817150.3170.9660.968
g694720.038694301697566920.0032970292570707910.3090.9910.971
g66721.3680083748367479e-091.618944822292009e-110.3071.00.997
g835222.005242785423931e-064.360513157652631e-080.3041.01.0
g159327.340042870600207e-152.2801908325829045e-170.2711.00.997
g1409622.517507127843448e-112.0482676336004385e-130.271.01.0
g936921.0418064959204795e-126.472762252760375e-150.2691.01.0
g579224.4503429426750643e-113.818341578034818e-130.2661.01.0
g189921.7082023642979344e-111.2887325529466665e-130.2541.01.0
g270520.00151265314796163227.182864800232011e-050.2540.9910.987
g905622.1052205881439083e-092.5536699441982322e-110.251.00.997
g936623.202325616504024e-094.168707903141333e-110.2391.00.997
g1362626.0026123085134e-106.304518844740406e-120.2381.01.0
g224623.361707618901228e-103.331869977313347e-120.2371.01.0
g628720.02554469584188510.00197631300670205730.2340.9910.984
g720821.7956500987760836e-063.878179207415802e-080.2321.00.997
g1163924.5416765355826236e-086.987194670127114e-100.231.01.0
g347724.682653568518168e-051.5031595035036132e-060.2291.00.994
g186321.8625732032653426e-055.317701601038627e-070.2271.01.0
g1125320.0055857744477131660.000332171794079984140.2240.9910.994
g1350921.767284129778137e-054.918410856091491e-070.2211.01.0
g116820.000264726952495954251.0103484281650324e-050.2211.00.997
g1022521.8047981791542744e-055.126053999964802e-070.2171.00.997
g365420.0244498333902105450.00188437325389048740.2130.9230.958
g1212420.000131072683946304254.595299718235815e-060.2110.9911.0
g1339521.850812848983689e-111.4237021915259147e-130.211.01.0
g1348427.128408848349637e-071.4024828059622808e-080.2041.00.997
g1292623.295522029063911e-076.1912913859632645e-090.2031.01.0
g1300720.0430875839579953760.0037287332271342150.2031.01.0
g1172320.031428261492301360.00257098056290571780.2010.9910.984
g1277821.2187042127315283e-062.5419718046619153e-080.1991.00.997
g1002422.2586466376669946e-074.009431901184014e-090.1981.01.0
g651522.9212832282945878e-084.278210644987636e-100.1961.01.0
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.