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Sample information : Ellobius_talpinus



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.
690

Estimated number of cell

8,312

Median UMI counts per cell

1,098

Median genes per cell

56,085

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
Ellobius_talpinus
Species
Ellobius_talpinus
Estimated number of cells
690
Mean reads per cell
56,085
Mean UMI count per cell
8,567
Median UMI counts per cell
8,312
Total genes detected
5,372
Mean genes per cell
1,108
Median genes per cell
1,098
Fraction reads in cells
99.15%
Sequencing saturation
37.84%
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
52,176,346
Reads pass QC
93.96%
Reads with exactly matched barcodes
97.44%
Reads with failed barcodes
2.56%
Reads filtered on low quality
0.0%
Q30 bases in cell barcode
87.80%
Q30 bases in UMI
87.84%
Q30 bases in reads
93.92%
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
49,026,000
Reads mapped to genome
80.74%
Plus strand
45.89%
Minus strand
54.11%
Mitochondria ratio
0.00%
Mapping quality corrected reads
0.66%
Reads mapped to exonic regions
25.6%
Reads mapped to intronic regions
0.4%
Reads mapped antisense to gene
0.5%
Reads mapped to intergenic regions
74.0%
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
g435800.076344050768866730.0103360434539956742.6050.1570.034
g72400.0550384604161602150.0070029055002669052.5750.1620.032
g87000.00350242909305808950.00028548626802262762.4570.2310.059
g534001.1364246471720005e-233.6148696530322085e-262.3190.7780.346
g257100.0155667532745249370.00156905445530499862.2190.2080.056
g570000.065894007259431720.0085806311640015452.1910.1710.044
g337700.0100948543029997470.00095329141032303782.1220.2180.056
g31700.00073180688412410034.6701791213486316e-052.110.2640.064
g103500.034032889622832520.0039310355608082892.10.1940.054
g303100.00168470271130516190.000120240213391362442.0210.2690.086
g362400.0038727929861167970.00031721485293839372.0190.2450.071
g305400.000158715131498430078.771929732915221e-062.0120.2960.078
g69500.020108313218918040.002134759296004422.0020.2130.066
g374206.107662004112607e-101.0806797581829465e-112.00.4860.169
g319703.871264424254696e-061.516181096576889e-071.9560.3840.137
g355200.0213637949852038720.00232750688904407971.940.2080.061
g243000.0060190827893182890.00052293025426085331.9260.2360.066
g504500.0294132169718497770.00332809736721163431.8620.2080.066
g307901.7458950005169571e-131.8743206764993176e-151.8520.6340.301
g295702.5253998932852088e-123.26343922591528e-141.8480.6110.275
g67801.4380989120111837e-235.14627841276368e-261.830.8380.466
g125900.000358661910812619152.1391366450056808e-051.8290.3190.118
g304800.034143018167318960.00395440224039466951.8270.2080.069
g329604.2526780614018115e-162.9591199234406245e-181.8210.7180.375
g280500.0090928740727544650.00083878599796383141.8140.2410.078
g289805.499904398967641e-071.8260119972715627e-081.8130.4070.132
g75004.8917343491493915e-052.431279497589161e-061.8030.3520.125
g182300.00043138263907479522.6157396603938873e-051.7720.3060.103
g56902.9798327729143386e-087.701357067174235e-101.7660.4680.181
g315801.8693555591087755e-227.432825284726741e-251.7260.8150.495
g259700.066428286454453260.0086634107185131881.710.1850.056
g245302.3621288711768176e-253.75686500385975e-281.7080.9030.613
g541200.0083561383963864120.00075421209382891271.7060.2640.103
g130206.725267222638824e-062.7275437642511334e-071.7040.3940.152
g104000.07458176533260360.0099801772774424181.6990.1850.059
g252804.021530183556603e-153.038134134694849e-171.6960.6810.348
g2700.00325578773928183240.00026408775300735341.6930.2690.091
g322307.10688378644632e-053.7017963261410254e-061.6870.3560.145
g133800.038638198281123220.0046012486621059261.6820.2180.083
g490500.091620018985604820.0128778038613961461.6820.190.071
g148403.5512556652160467e-106.1423308722424664e-121.6740.5560.243
g308101.7540619878257145e-262.0923204626151664e-291.670.9310.645
g201807.347471355504753e-091.6798393755130152e-101.6670.5090.201
g276902.0372040406763773e-171.2150322310197082e-191.6610.7960.471
g180005.478893282463759e-127.297929421969619e-141.6470.6390.287
g262701.0449957072958353e-063.6148956872659116e-081.6340.4720.221
g200100.089692250485826480.012535517314420681.630.1810.059
g557201.87958815429113e-151.3825996363572926e-171.6270.7640.444
g326300.0117430480120822060.00112761276139874861.6070.2640.108
g7200.0150002215776605680.00149165581564630891.6040.2550.105
g361814.488192325581599e-087.049049576957183e-100.5390.9670.973
g555410.000288330109495087961.4043911893895934e-050.460.8530.864
g193410.000101744155381183164.303439440254605e-060.4580.9670.955
g212510.00109935801121737666.403815055401419e-050.4390.9950.984
g559613.5555828091845584e-051.3006505703577708e-060.4091.01.0
g225810.0289180891081224460.0032597527881322920.3940.6740.684
g496513.430353189228286e-069.343109083981614e-080.3770.9950.995
g549110.00263098464788284830.000179932150869125210.3550.8150.861
g267212.792789088851821e-059.883030970489545e-070.3320.9950.984
g492710.028322754183034820.00313633679521876630.3310.8260.802
g420613.219372092979606e-254.131944241059094e-280.3291.01.0
g274612.15863479325084e-101.9311842086737136e-120.3181.01.0
g467416.964790784117899e-052.7693005105836576e-060.3160.9570.973
g478610.039728754944556140.0048811869892118680.2990.9840.957
g267612.036046384478197e-164.857367120027508e-190.2721.01.0
g53010.0181777847743098860.00183794384845346450.270.8910.914
g212718.042044676868227e-081.406958114442155e-090.2451.01.0
g338014.022943557014644e-104.078928855024788e-120.241.01.0
g190112.7883895631538865e-102.6470610040008513e-120.2341.01.0
g29010.0090810529559467620.00076728578653625720.2320.9950.984
g277616.446866879013781e-071.4611189348063042e-080.2271.01.0
g540711.0424361541397707e-124.5593629008101304e-150.2241.01.0
g429312.124407789186233e-101.8583288811967048e-120.2171.01.0
g383312.8744515995032823e-121.3715077214329778e-140.2161.01.0
g160416.429169973194596e-081.059262108736309e-090.2071.01.0
g20715.507910871847004e-123.0660338849247735e-140.2011.01.0
g90010.00052300886794887032.7242211412048513e-050.1980.9950.995
g126611.5791015795647468e-135.964797219031847e-160.1951.01.0
g57412.7883895631538865e-102.6608886487353192e-120.1941.01.0
g455014.266684849625171e-095.598433401098634e-110.1941.01.0
g503010.0474797444432492540.0061072355178493570.1920.9080.952
g540918.741232269354019e-053.5799082455008505e-060.1851.01.0
g520810.087530893238360930.0133471560862470830.1840.9620.948
g461010.026706083213349430.0028723640195670060.1820.9890.995
g31015.455204943003188e-071.2038325023327116e-080.181.01.0
g507511.5714942832336566e-063.936546315853693e-080.1791.01.0
g319110.054805622574225910.0073328397599312190.1750.8320.893
g273411.8006085474771143e-064.617862875239518e-080.1711.01.0
g230011.0521665413362866e-108.576307792204325e-130.1691.01.0
g275412.0433745240405474e-073.940503555306821e-090.1671.01.0
g174110.047506415277278950.0061299092758901770.1670.9780.982
g182213.6891693004985295e-061.03591477475792e-070.1651.01.0
g334515.176643611485123e-071.1320691794500272e-080.1621.01.0
g512910.031847853133764330.0036913118045695040.1611.01.0
g427414.850721735227776e-061.388675804916103e-070.1591.01.0
g33011.3929072083662609e-091.6338275406284173e-110.1581.01.0
g226613.915105366473652e-095.0592812886836456e-110.1441.01.0
g439410.09833594005103720.015600811165154610.1420.9510.968
g263616.964790784117899e-052.766008743243836e-060.141.01.0
g29310.0035925064852459530.000257117760375455860.1371.01.0
g161620.00032536226988840341.2160657403383665e-056.8490.2560.004
g120521.872293538386491e-073.0894704510154823e-095.5750.3520.01
g489020.00223648957570585960.000106347143314461154.9770.2320.008
g72921.3651317783632825e-081.682667400765875e-104.9520.3840.014
g384625.593042891240205e-163.002229782574265e-184.8630.5280.026
g26426.137529327578371e-447.321108541842987e-474.8130.880.118
g160622.248587144969747e-383.57628174150258e-414.7480.8240.086
g559425.738104403719198e-144.334949648932993e-164.7060.4960.03
g165826.542808717176934e-222.3082122405141204e-244.6250.6240.044
g443321.7334186698526663e-225.169240566161032e-254.610.640.07
g333223.7073168544974204e-142.5796439345409488e-164.4320.5040.034
g53823.603541048688306e-357.164097512302795e-384.2040.8080.114
g533522.367262250055514e-056.259361416647781e-074.0780.3120.026
g141624.8012797501587e-078.877117629518074e-094.0540.360.03
g242522.2562224748100652e-141.480225480491693e-164.0410.520.052
g33121.0169070218236827e-184.649873062016839e-214.020.5920.056
g150620.00105873229257987064.693783324956484e-053.9280.2560.022
g123020.0063477139661714810.000364709609587188463.8530.2240.018
g370920.047080545942637670.0039311787864627883.7080.1840.018
g339720.057957452181757880.0051389709091578563.6750.1760.014
g570221.71206257436229e-363.0633326380239785e-393.5630.8640.236
g368221.790910791647816e-054.5573873028015993e-073.5010.3280.038
g213522.532467038285332e-236.545143438908413e-263.4720.6960.122
g548923.679401216283656e-152.1213247569031022e-173.4340.6240.216
g429020.0088998044278795360.00054672754835283843.3430.2320.034
g426120.090106074783381940.0086344190945507143.3430.1680.016
g536520.00145090679979483136.547829891718225e-053.3040.2640.036
g59723.742551152606929e-084.910703301631358e-103.2720.4080.048
g527121.0902841909464712e-451.0837815019348619e-483.1740.9520.423
g558323.331591865152137e-059.272820300622251e-073.160.3280.05
g189629.669377587516378e-483.8446829373822576e-513.1031.00.551
g132520.0518495087438029450.0044633871344068942.9620.1920.028
g497220.0029636507998777550.000146709552518799422.9570.2560.036
g47021.7680557453193429e-101.7575106812319511e-122.8820.4960.106
g400421.3382546987148179e-053.272471728467646e-072.8220.3520.056
g200320.0369478786376455650.0029308555817933562.7970.2080.038
g468726.162489830321298e-051.8499720961799522e-062.7940.3360.068
g474022.417932543684588e-056.44141075255934e-072.7920.3440.058
g223120.053567588240339330.00468583276853862952.7870.1920.028
g535920.0061659468059798730.000351814459903821832.750.2480.044
g410920.000225247524157444267.747081844778898e-062.7040.3120.052
g76120.042197127701919450.00341131517661206772.6750.20.03
g360429.854895142176138e-242.3510684235807884e-262.6360.7840.269
g422722.6183138601640676e-092.9150213950136737e-112.5490.4880.11
g357720.0058192683842591840.000326249241423675952.5140.2560.048
g371628.532679885913491e-232.374900962282085e-252.420.8160.337
g285723.482755613095284e-068.031802209126301e-082.4170.4080.12
g478720.0128860936960954590.0008488376797039062.4070.240.046
g568120.00247832833668725030.000120221096252820872.4060.2880.07
g203923.9602527819535425e-497.873265968098495e-532.4021.00.842
g138130.00735940212128205740.000103880228749706981.3090.4340.177
g534836.134547376194786e-093.65877577109033e-121.2370.8590.579
g432934.514654593939711e-051.795091289836863e-071.1440.7270.39
g475730.036804052379495590.00075364162924215631.0940.4340.217
g97131.1446994238876911e-069.102977525945853e-101.0410.9190.695
g334138.21633323251965e-054.083664628488892e-070.9820.8590.587
g272230.08320463506922290.00238605424228807750.9350.4340.219
g174630.053900740698844060.00129661821561831640.9020.4950.305
g284830.046869592308245840.0010529351751156620.8990.5450.354
g8330.0052520416348494666.578103836888993e-050.880.6770.413
g528330.00029924345280350482.2606861245592805e-060.8740.8180.552
g397130.004865247413980675.996925241884722e-050.8390.6970.49
g420230.017332603211606370.000296342718926073140.8140.6460.398
g428931.246040760032246e-053.37348106934408e-080.8020.9190.787
g49030.045048951929638750.00100307805489454090.7560.6570.413
g224535.79989436564411e-052.536733122150505e-070.7440.980.857
g460430.0149893489846410960.000250319148053648540.7440.7070.495
g326730.075697819821883560.0020617497645324150.7430.5450.36
g548130.0067507765789122888.99208808721915e-050.7320.7780.592
g70030.0277201674480408930.00051251999456616360.720.7470.52
g189630.0130912054723567630.0002108126527357650.7130.9090.59
g114431.4549529822281908e-061.4462753302467105e-090.7110.990.909
g559330.08320463506922290.0024150848350112410.70.5860.415
g463730.00738474788862328050.000107174273532703680.6990.7780.606
g276330.096795144867339950.0030019965406173030.6970.5350.343
g144230.030735926011909070.00058282822847879570.680.6770.503
g548432.2524257729616173e-108.955967288117763e-140.6771.00.992
g464730.063530635486025870.00163853378903601030.6690.6870.472
g46330.036353635225360810.00073719101252222720.6620.6970.535
g42030.085388089371289040.00252938873087913850.6490.6360.432
g13930.085388089371289040.00252685212843651530.6480.6670.476
g218130.072806291093152440.00192509676250283780.6330.7780.568
g251530.072858596467532220.0019409645977434030.6280.6460.488
g280230.0574949380316339550.00142880064690939260.620.7370.543
g508330.000380531189780806553.0260929604835508e-060.610.970.859
g53230.0111005271055746730.000172135410384656970.6090.9290.775
g545030.000360817083537705552.7975877252426474e-060.6080.990.884
g94830.00276294797012970963.0211160707183705e-050.6060.9190.811
g377031.4448761644756415e-054.308775838396545e-080.5981.00.97
g149530.050067675490279920.00115959693541411720.5930.7980.606
g470130.057823023857383330.00144844950418097420.5880.7680.589
g188431.246040760032246e-053.4681054951195714e-080.5870.990.952
g266630.030735926011909070.0005920563145411910.5860.9190.739
g98530.009114074425035450.000139519628375294160.5810.8690.752
g88630.044386677723232980.00096477572027828970.580.8180.669
g156730.076068461348397440.00210209068139706640.560.8480.67
g174230.000219400970882723931.439409948137155e-060.5521.00.947
g256230.0479292763710098750.00108626988196722190.5410.970.817
g130330.096795144867339950.0029901474133494660.540.8280.665
g196630.0326399932487110.00064241736215156840.5310.9490.834
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.