SRR9985509

Alerts

The analysis detected 1 warning and 1 informational notice.
AlertValueDetail
Low Fraction Reads in Cells50.3%Ideal > 70%. Application performance may be affected. Many of the reads were not assigned to cell-associated barcodes. This could be caused by high levels of ambient RNA or by a significant population of cells with a low RNA content, which the algorithm did not call as cells. The latter case can be addressed by inspecting the data to determine the appropriate cell count and using --force-cells.
Intron mode usedThis data has been analyzed with intronic reads included in the count matrix. This behavior is different from previous Cell Ranger versions. If you would not like to count intronic reads, please rerun with the "include-introns" option set to "false". Please contact support@10xgenomics.com for any further questions.
1,305
Estimated Number of Cells
9,524
Mean Reads per Cell
1,105
Median Genes per Cell

Sequencing

Number of Reads12,429,323
Number of Short Reads Skipped0
Valid Barcodes91.7%
Valid UMIs100.0%
Sequencing Saturation26.0%
Q30 Bases in Barcode93.5%
Q30 Bases in RNA Read87.0%
Q30 Bases in RNA Read 288.0%
Q30 Bases in UMI93.2%

Mapping

Reads Mapped to Genome91.4%
Reads Mapped Confidently to Genome84.0%
Reads Mapped Confidently to Intergenic Regions4.5%
Reads Mapped Confidently to Intronic Regions11.4%
Reads Mapped Confidently to Exonic Regions68.1%
Reads Mapped Confidently to Transcriptome74.0%
Reads Mapped Antisense to Gene5.0%
 

Cells

110010k110100100010k
CellsBackgroundBarcode Rank PlotBarcodesUMI counts
Estimated Number of Cells1,305
Fraction Reads in Cells50.3%
Mean Reads per Cell9,524
Median UMI Counts per Cell1,996
Median Genes per Cell1,105
Total Genes Detected21,528

Sample

Sample IDSRR9985509
Sample Description
ChemistrySingle Cell 5' PE
Include intronsTrue
Reference Path
‎/home/ah3q/sra2json/genomes/CellRanger/hg38‎
TranscriptomeGRCh38-2020-A
Pipeline Versioncellranger-7.0.1