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Sample information : FFPE-breast



Estimated Number of Cells
The total number of barcodes identified as cells.
Mean Reads per Cell
The number of reads that mapped to a unique gene in the transcriptome divided by the number of barcodes associated with cell-containing partitions.
Median UMI Counts per Cell
The median number of UMI counts per %s cell-associated barcode.
Median Genes per Cell
The median number of genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count.
5,005

Estimated Number of Cells

8,947

Mean reads per Cell

2,822

Median UMI Counts per Cell

1,709

Median Genes per Cell

Cells


Estimated Number of Cells
The number of barcodes associated with at least one cell.
Fraction Reads in cells
The fraction of valid-barcode, confidently-mapped reads with cell-associated barcodes.
Mean Reads per Cell
The number of reads that mapped to a unique gene in the transcriptome divided by the number of barcodes associated with cell-containing partitions.
Median UMI Counts per Cell
The median number of UMI counts per %s cell-associated barcode.
Median Genes per Cell
The median number of genes detected per cell-associated barcode. Detection is defined as the presence of at least 1 UMI count..
Total Genes Detected
The number of genes with at least one UMI count in any cell.
Barcode Rank Plot
The plot shows the count of filtered UMIs mapped to each barcode.
Sample Name
FFPE-breast
Species
Human
Type
FFPE
Organ
Breast
Estimated Number of Cells
5,005
Fraction Reads in cells
61.72%
Mean Reads per Cell
8,947
Median UMI Counts per Cell
2,822
Median genes per cell
1,709
Total genes detected
44,107
Sequencing & Mapping


Number of Reads
Total number of read pairs that were assigned to this library in demultiplexing.
Valid Barcodes
Fraction of reads with barcodes that match the whitelist after barcode correction.
Valid UMIs
Fraction of reads with valid UMIs; i.e. UMI sequences that do not contain Ns and that are not homopolymers.
Sequencing Saturation
The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid cell-barcode, valid UMI reads that had a non-unique (cell-barcode, UMI, gene).
Q30 Bases in RNA Read
Fraction of RNA read bases with Q-score ≥ 30.
Reads Mapped to Genome
Fraction of reads that mapped to the genome.
Reads Mapped Confidently to Genome
Fraction of reads that mapped uniquely to the genome.
Reads Mapped Confidently to Transcriptome
Fraction of reads that mapped to a unique gene in the transcriptome. These reads are considered for UMI counting.
Reads Mapped to Exonic Regions
Fraction of reads that mapped to an exonic region of the genome.
Reads Mapped to Intronic Regions
Fraction of reads that mapped to an intronic region of the genome.
Reads Mapped to LncRNA Regions
Fraction of reads that mapped to an lncRNA region of the genome.
Sequencing
Number of Reads
244,817,939
Valid Barcodes
91.48%
Valid UMIs
100.0%
Sequencing Saturation
53.74%
Q30 Bases in RNA Read
89.31%
Mapping
Reads Mapped to Genome
65.54%
Reads Mapped Confidently to Genome
38.08%
Reads Mapped Confidently to Transcriptome
34.45%
Reads Mapped to Exonic Regions
13.94%
Reads Mapped to Intronic Regions
47.91%
Reads Mapped to LncRNA Regions
10.03%
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 differential expression analysis seeks to find, for each cluster, features that are more highly expressed in that cluster relative to the rest of the sample. Here a differential expression test was performed between each cluster and the rest of the sample for each feature. The Log2 fold-change (L2FC) is an estimate of the log2 ratio of expression in a cluster to that in all other cells. A value of 1.0 indicates 2-fold greater expression in the cluster of interest. The p-value is a measure of the statistical significance of the expression difference that by a negative binomial test, and been adjusted for multiple testing via the Benjamini-Hochberg procedure reported as p_val_adj. The pct.1 is the percentage of cells where the feature is detected in that cluster. And the pct.2 is the percentage of cells where the feature is detected in the rest of the sample. The features were filtered by p_value < 0.01, p_val_adj < 0.1, pct.1 ≥ 0.1, pct.1 ≥ 0.1, and avg_log2FC > 0.25 for each cluster were retained. In this table you can click on a column to sort by that value.
gene cluster p_val_adj p_val avg_log2FC pct.1 pct.2
ERBB4cluster1002.564937794251560.9980.872
AFF3cluster1002.149906206714520.9950.853
TRPS1cluster1001.7107454288703210.929
TTC6cluster1001.597281635760420.8760.311
PRLRcluster18.02383074372159e-2912.42705104165807e-2951.618976270190050.9110.387
LIMCH1cluster13.48511114845395e-2761.05417760086327e-2801.800820149779530.9540.569
LINC00504cluster19.88088095293193e-2742.98877221806773e-2781.68118024807520.8870.381
LINC00993cluster11.63910724787459e-2434.95797715630549e-2482.561905675932550.9620.776
THSD4cluster11.1926288483166e-2413.60746778075197e-2461.738342353658460.970.691
ANKRD30Acluster15.44596305191829e-2371.6472967489166e-2412.042967293022410.7670.277
LYPD6Bcluster13.66110422516432e-2261.1074120463292e-2301.278495240710270.7330.231
DLGAP1cluster11.21816299587528e-2193.68470355679152e-2241.53983227218950.9080.547
RASEFcluster14.45551154598298e-2161.34770464185813e-2201.129731166331750.6870.191
DACH1cluster18.27224595990357e-2082.5021917604064e-2121.315978838965890.7630.282
VTCN1cluster17.20922589100762e-2022.18064908983897e-2061.963872264553840.8450.435
ANKS1Bcluster13.65964297944147e-1961.10697004822791e-2001.28857562390850.9260.576
ARHGEF38cluster11.87948666453032e-1955.68507763015826e-2001.056924426945830.6890.212
INPP4Bcluster13.80530226985825e-1941.15102911973934e-1981.34431393024250.940.607
MALAT1cluster19.41404887315056e-1922.84756469242304e-1960.63027640619408611
MYO6cluster11.45646256800359e-1904.40551290987173e-1951.159383658471240.8120.361
AK5cluster12.68682779844627e-1818.12712582712119e-1861.271929088127610.8760.461
SHROOM3cluster11.06611866442783e-1803.22479934793657e-1851.254549346135340.9050.535
EFHD1cluster13.57276437628024e-1791.08069097891114e-1830.8626522545935630.570.138
TMC5cluster12.67409662810145e-1768.08861653993179e-1810.9018160241712820.5640.138
RERGcluster11.2207552701699e-1643.69254467685995e-1691.256851149550730.8480.449
ALCAMcluster11.87191948306857e-1625.6621883940368e-1671.204108685140220.7770.358
ST8SIA6cluster13.18212679413408e-1629.62530790724163e-1670.9867492240354580.6370.205
NEBLcluster16.24776638856423e-1541.88982649381858e-1581.009258133213120.8760.483
RBM47cluster11.29999101708914e-1493.93221723257452e-1540.9924963691763550.8280.409
ESR1cluster11.32732625873317e-1494.01490096410517e-1541.741414052843830.8530.504
NAALADL2cluster14.912055323995e-1431.48580015849818e-1470.9380106434329540.970.719
AGAP1cluster13.34688833389558e-1411.0123679170888e-1450.9295508401829840.9550.69
TBC1D9cluster13.06057724742224e-1399.25764442656454e-1441.161837260698390.8130.471
MAGI3cluster11.40532465784319e-1364.25083078597456e-1410.965256704448610.6890.287
SYTL2cluster11.53313375705229e-1344.63742818225133e-1390.9820447658795850.6190.223
ARcluster13.32375864235429e-1341.00537164015556e-1380.8800536825610370.5520.174
SIDT1cluster11.42549545802793e-1334.31184349070759e-1380.7782823997970860.6010.199
RAB11FIP1cluster18.72616795166329e-1292.63949423825266e-1331.191628789838110.6890.31
NEK10cluster13.90653031886899e-1271.18164861429794e-1311.310016184233950.6730.3
MLPHcluster12.08770858774312e-1266.31490800890235e-1310.6797424466996570.5170.154
CAPN8cluster17.93583189481374e-1262.40043312002836e-1300.5498081746100680.3790.075
CASZ1cluster18.0284747964805e-1242.42845577630989e-1280.7222281901762650.6250.232
CADPS2cluster14.31198956446133e-1231.30429206426538e-1270.8972472313811490.8070.434
ARFGEF3cluster17.49210574295276e-1222.26621468328879e-1260.6973170753446210.5590.185
LRP2cluster11.94570588382704e-1215.88537774902311e-1261.111608305852260.6070.242
ADGRV1cluster13.14268192689148e-1219.50599493917567e-1260.755305001128590.6550.268
KIAA1217cluster19.17124451771945e-1212.77412114873547e-1250.85669873631670.9930.87
GLI3cluster14.38933167922606e-1191.32768653334121e-1231.043251359966890.8780.586
ENSG00000231482cluster14.52806772411533e-1161.36965145920004e-1200.6803741237759170.4430.118
NTN4cluster11.53198544323333e-1114.63395475872151e-1160.9944779923973470.7710.425
TBX3cluster12.9894903010555e-1099.04262039036751e-1140.5935797943535390.410.104
MAST4cluster11.45667663173765e-1084.4061604105797e-1130.9233426470063020.8290.51
LYPD6cluster12.81797049331046e-1078.52380669482897e-1120.800928187457440.4580.136
KCNC3cluster11.01427378678424e-1053.0679787864012e-1100.5249813442067920.4330.117
ATRNL1cluster11.06666418690579e-1053.226449446176e-1100.904653638694580.6220.269
XBP1cluster11.28063233197571e-1043.87366101626046e-1090.5560271547932410.4350.121
PATJcluster11.87170804600631e-1045.6615488384946e-1090.8104271157152190.8920.61
NCKAP5cluster16.14693881881494e-1041.85932813636265e-1080.8921571957544820.8210.509
GPR39cluster11.01669673299378e-1033.07530772230423e-1080.8386252236451930.5210.191
VN1R53Pcluster11.73459848643517e-1035.24681937820682e-1080.3503413949992350.2170.022
MYO5Bcluster15.58995125712697e-1031.69085035000816e-1070.7675961017239540.7810.429
ENSG00000250195cluster17.84028882651868e-1012.37153322036258e-1050.8523140627537080.4770.162
MAPK8cluster16.60815748561239e-971.99883771494628e-1010.8389573511827750.7310.394
NFIAcluster11.14329664389368e-963.45824756168688e-1010.727935501137630.9430.722
CTNND2cluster11.5968641851413e-964.83020019703964e-1010.8428772414610850.6480.315
LINC02343cluster11.3932383263822e-944.21427200962552e-990.7445003416224820.530.205
APBB2cluster14.21624192403185e-931.27533028555107e-970.8586208940778290.8060.492
PTPRKcluster16.87982902839811e-932.08101301524444e-970.7921629860699290.8740.601
CYP4Z2Pcluster11.15774988844777e-903.50196578477849e-950.5935595188257660.3190.072
NOSTRINcluster14.83381164904344e-901.4621329851916e-940.4955348489529520.3340.08
AGR3cluster14.16373422989445e-881.25944774043994e-920.3669919646344270.2190.03
TSPAN15cluster19.10097202251773e-882.75286510058008e-920.4674168044866670.3430.085
NEDD4Lcluster13.30849199673828e-871.00075378001763e-910.7321621136695630.8770.625
ADAM10cluster15.7503128716262e-871.73935658548887e-910.8343692909454650.6540.327
SAMD12cluster11.00577869762145e-863.04228281192211e-910.6978511306208530.7730.441
FARP1cluster11.2317026374638e-853.7256583105378e-900.8010565845611820.7320.415
ELAPOR1cluster17.80131445735609e-852.35974423997462e-890.5994839081964560.520.204
KIF16Bcluster16.209799976753e-841.87834240071174e-880.695874924908560.7680.435
BCL2cluster11.07131770744109e-833.24052543085628e-880.775653837733890.9040.687
TOX3cluster11.12866305077625e-833.41398381964989e-880.5703867675104160.3350.087
STC2cluster13.4942863537473e-831.05695292006875e-870.7132982232969880.3780.114
GALNT7cluster14.13031102353932e-831.2493378776586e-870.6569453000458190.5390.223
GATA3cluster17.83395456779567e-832.36961723163813e-870.5968564220502260.4910.186
ENSG00000259354cluster15.00099477542818e-821.51270259389842e-860.455395531346070.2980.068
REREcluster15.92503514935562e-811.79220663924853e-850.634593396289770.9120.689
PBX1cluster16.09077633224556e-801.84234008839854e-840.7212508971531490.9540.776
DCDC2cluster12.71644513522973e-798.21671244776082e-840.6809456444417260.3540.102
ENSG00000255367cluster13.56294626070934e-791.0777211919871e-830.3593782684063220.2770.059
PCSK6cluster16.77606564909656e-792.04962663312056e-830.6024043349331510.4520.164
CA12cluster19.87250759105843e-792.98623944073153e-830.5020373637233110.3910.121
EPB41L4Bcluster15.05715354781746e-761.52968951839608e-800.438527515464990.3320.091
LINC00862cluster11.07555084645925e-753.25332984409937e-800.4876786727089310.4070.137
ENSG00000234918cluster18.57002319454552e-752.59226351922127e-790.2576506973016050.1740.02
ACADSBcluster11.19965913388405e-743.62873301235345e-790.6021640605441640.4140.146
TFAP2Bcluster12.4225969107641e-737.32787934290411e-780.4516453446885170.3580.108
RAB27Bcluster13.77674663919509e-731.14239160290233e-770.5169296873869180.4210.148
MAP3K1cluster11.61865231827525e-724.89610501595661e-770.6559781668654810.6520.337
MAGI1cluster16.21050099871228e-721.87855444607147e-760.5465619681492730.9570.744
CACNA1Dcluster17.46843233265287e-722.25905394212125e-760.6784654933752970.5990.293
LRBAcluster13.233347883653e-719.78024163234423e-760.5748067172520420.9070.678
ICA1cluster13.49126105166223e-711.05603782566916e-750.5106291570855570.4570.175
AZGP1cluster16.48797651813552e-691.96248533518921e-730.461383180245910.3890.132
SHANK2cluster11.59901307825176e-684.83670017620013e-730.5656819511721580.8290.534
TM4SF1cluster17.51341049556674e-682.27265895207705e-720.6164097116997120.4450.178
EPB41L5cluster19.86518031753101e-672.98402308455263e-710.4529274790401480.4010.143
NAV3cluster11.44881585524582e-664.38238310721662e-710.8330390392023020.8180.607
SLC4A8cluster11.8839943177428e-665.69871239486631e-710.3955601049199360.2910.078
FOXA1cluster11.15662396881361e-633.49856009925472e-680.2923109215524990.2260.047
CPHL1Pcluster11.68698210964213e-635.10278920036941e-681.327183107041350.4390.194
NCAM2cluster13.56165047137514e-631.0773292411903e-670.6510884537324840.5190.248
GSE1cluster17.17974775962451e-632.17173253467166e-670.6697821715084510.810.564
RAPH1cluster17.68112352733833e-632.32338884674481e-670.5341478866625440.5590.269
DHCR24cluster18.15464952294802e-632.46662115031701e-670.3657666634544630.3180.096
VMP1cluster12.8883805366805e-628.7367832325484e-670.6254886783148580.6670.389
ATF3cluster11.66347305854576e-615.03167894296962e-660.7465218987636730.4940.237
MRTFBcluster12.33596346992338e-617.06583021755408e-660.5588705069994930.6620.374
BHLHE40cluster17.18629360168876e-612.17371252319684e-650.4536548329386620.4150.16
KDM4Bcluster17.63496836813191e-612.3094278185517e-650.5569732422776830.6380.349
LDLRAD3cluster13.88017330717649e-601.17367613647202e-640.6150342487907510.6210.338
IL20RAcluster15.4805240210822e-601.6577507625778e-640.2988219006316470.2230.049
CLSTN2cluster11.48783642999537e-594.50041267391219e-641.258739318222440.5960.357
SH3RF1cluster12.58025665393605e-597.80476906816711e-640.6044582520531550.6260.344
WWC1cluster16.08464791948937e-591.84048636403187e-630.5772371330203210.5190.25
RAD51Bcluster11.09036238650499e-583.29813184060797e-631.012946322722850.9030.756
KRT19cluster11.49926890113778e-584.53499365135445e-630.3090786876422750.2410.059
NPNTcluster12.26906082856877e-586.86346288133323e-630.3790833818596220.290.085
PPP1R9Acluster12.37148436642293e-587.17327394562291e-630.4956070315155880.5350.255
MYO5Ccluster16.01657981101596e-581.81989709952086e-620.4012293679149690.4510.187
CDYL2cluster18.38909683341632e-582.53753685221304e-620.4771343001977260.3960.154
DNAH5cluster16.26886971986594e-571.89620983662007e-610.4815194014363460.4140.167
C1orf21cluster12.57400563241244e-567.78586095708543e-610.588877703090150.7470.474
SCUBE2cluster14.06211609497446e-561.22871025256336e-600.4396969032363590.3040.096
KIF13Bcluster18.51572114061869e-562.57583821555314e-600.5495264813332420.5710.294
CSNK1A1cluster11.18390728014565e-553.58108675180171e-600.4758615556705530.5150.242
RHPN2cluster11.2213928801099e-553.69447332156654e-600.3143490415697210.2680.074
MPP7cluster11.39924849568791e-554.23245159010257e-600.4268883281630090.5080.232
ELOVL5cluster14.25258262852477e-551.28632263415752e-590.6878015334887640.6530.395
PKP4cluster14.66246475620687e-551.41030391899784e-590.539518679687870.7970.523
LRIG1cluster16.35897288696167e-551.92346427312815e-590.5772557103744380.650.376
FHITcluster11.03041268215166e-543.11679577178361e-590.6113288122143790.9190.771
TMEM241cluster11.09426156282685e-543.30992608235587e-590.4653985209001020.4510.198
MACC1cluster12.41414305508383e-547.30230809160263e-590.6059538444570820.4980.243
MTUS1cluster17.07668944962939e-542.14055942215045e-580.4657807758744530.6020.314
C3orf52cluster11.23806220030475e-533.74489473776392e-580.2979703612313490.2240.055
SLC7A2cluster11.19790347282207e-523.62342248282539e-570.4715349311813560.3050.103
PLATcluster11.60153041976639e-524.84431463934178e-570.5567402300764350.370.145
TFAP2Acluster17.29847732013208e-522.20764589235695e-560.3343099845236760.3040.1
LINC01876cluster17.57979420726935e-522.2927387196822e-560.6100563355919750.6440.382
WWP1cluster11.01251080061131e-513.06264609985273e-560.4665846696426120.6140.337
PI15cluster17.1178490739813e-512.15300939926839e-550.7669513788745910.2750.09
VAV3cluster19.39045902849914e-512.84042922822115e-550.5598626804676810.6740.406
LINC02899cluster11.10120134212425e-503.3309175502851e-550.5313304491052430.3780.156
RALGPS2cluster11.22162365984679e-503.69517138489653e-550.376583842338840.5320.26
ENSG00000257261cluster12.5204492798706e-507.62386352047975e-550.5959391042073530.7560.515
GALNT6cluster13.28213170591748e-509.92780310319866e-550.2800359442317580.2260.059
ENSG00000286171cluster14.29538812923052e-501.29927045651256e-540.44192530175405710.998
CAPN13cluster15.69998675692081e-501.7241339252634e-540.3574738846583140.290.095
ERBB2cluster11.35854444286677e-494.10932983323282e-540.2962050571493430.3030.101
PLEKHA6cluster13.28739087748746e-499.94371106318045e-540.3983498806091420.4220.183
SLC38A1cluster15.92020434104013e-481.79074541471268e-520.4877752201725450.610.341
MREGcluster11.30515248669185e-473.94782966331473e-520.3627934006024350.3020.104
BCL2L1cluster11.45945519396972e-474.41456501503244e-520.499982124094920.4850.243
KIAA1958cluster12.70910808613917e-478.1945193168154e-520.3268834405008170.3030.105
ARHGAP29cluster12.83724620034178e-478.58211191875917e-520.422780120289380.4110.181
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NLRP9cluster140.0005999994455994561.81488035571523e-080.2594155970601140.2370.044
IGHV4-39cluster140.0006734461143174562.03704208807458e-080.6602034762803720.1050.01
ZNF169cluster140.0009361843867881542.83177370474336e-080.546824620098850.5790.223
IGHV3-21cluster140.0009763066179601942.95313556551783e-080.7955553291752590.1050.011
CCDC61cluster140.001204654383683633.64384266087001e-080.2729734449520650.2110.037
ENSG00000255028cluster140.001449653911336834.38491806211987e-080.3126803388904420.3420.087
ENSG00000225205cluster140.002247788781507556.79911912131746e-080.2912635888307540.2370.047
ENSG00000235726cluster140.00243749921322527.37295587787416e-081.257769987125890.7630.413
RNA5SP202cluster140.002577103854679867.795232470296e-080.5545564251276270.7630.362
RYR2cluster140.003854986866116131.16605773324747e-070.6235083103138880.8680.451
IGHG1cluster140.004135415316449911.25088182590741e-072.973125373329790.6050.282
IGLV2-14cluster140.004520428446656191.36734072796618e-070.9406360164948130.1580.025
DUSP5cluster140.005036367689331781.52340220487955e-070.4245977635327450.3160.083
ENSG00000224271cluster140.005973102449658731.80674605252835e-070.5004934446822880.6840.296
HFM1cluster140.006379751864338761.92974950524463e-070.9530428596938720.6320.285
MTNR1Bcluster140.00737309595409452.23021656203705e-070.438507336955870.1580.025
ENSG00000287092cluster140.007591610548539482.2963129305927e-070.4177011495876880.5790.221
ENSG00000285703cluster140.007907379177369992.39182673241682e-070.6386315413865940.6050.272
RNA5SP79cluster140.007995983570448912.41862781925254e-070.4067282933379740.3420.095
ENSG00000261235cluster140.008999774752805352.72225491615407e-070.4558950357928460.4470.154
ENSG00000283907cluster140.01025364785431563.10152687668347e-070.7206259168487070.6580.364
RCHY1cluster140.01096164148013633.31568102847438e-070.6826279678296510.6580.309
LINC01630cluster140.01399062741702394.23188972081787e-070.4357946861683060.3950.122
OCRLcluster140.01490041511412164.50708261165201e-070.5125185706359060.6840.318
U2AF2cluster140.01598863602117754.83624804028357e-070.4795695188522490.5530.223
ERLEC1cluster140.01686650028505955.10178472022367e-070.385046440691970.2890.075
PTPRDcluster140.01691675169458945.11698478360237e-070.5048057829666890.8680.471
ENSG00000285040cluster140.0202370270178596.12130278822111e-070.3893537512379930.3680.114
TMC3-AS1cluster140.02081089260367896.29488584503293e-070.2892169188298560.2630.063
INHBAcluster140.02436215031035577.36907147923645e-070.4676482172185240.4210.141
SOX6cluster140.02625701756864837.94223156946411e-070.4050385306941660.5790.235
TRHDE-AS1cluster140.03064984996892939.27097700209598e-070.3682617729988450.3420.102
IGHG2cluster140.03298789299640769.97818904912509e-072.51451602532950.3950.144
ENSG00000237167cluster140.0409514183982561.23869989105433e-060.3204779310830210.3420.102
IGLV6-57cluster140.04353573260344751.31687031468383e-061.796820328561470.1580.028
OVCH1-AS1cluster140.04435976610107611.34179570783654e-060.2639207377281120.2110.045
ENSG00000228430cluster140.04443026662634741.34392821011335e-060.4419992585079230.5790.255
LINC02210-CRHR1cluster140.04964482425145511.50165832581534e-060.2742466057478060.2370.056
ENSG00000233611cluster140.05939279168081391.79651517485826e-060.3177207641124470.3680.116
ENSG00000256803cluster140.05973647619451771.80691095567204e-060.6035763001519850.4210.155
GLIS1cluster140.06071969096300461.83665126929839e-060.3920379623434280.4470.162
NRG3cluster140.06849108199023642.07172056836771e-060.7099720538980090.6320.317
CKAP4cluster140.08475056354261512.56353791719949e-060.31860919153850.3950.131
PIP5K1Bcluster140.09431793220385982.8529320085862e-060.5350153178092170.4740.189
Gene Body Coverage


geneBody
This plot illustrating the coverage profile along the gene body. Scaleing all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. The coverage was calculaterd for each position as (NUMi - min(NUMs))/(max(NUMs) - min(NUMs)). Here, NUMi denotes the number of covered reads of position i, min(NUMs) and max(NUMs) are the minimum and maximum number of covered reads in each nucleotide position.
Saturation


Left
The plot shows the Sequencing Saturation metric as a function of downsampled sequencing depth in mean reads per cell. 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. 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.