Table 3 Single cell gene expression (scRNA) sequencing summary metrics (N = 5 samples)
From: Single-cell T-cell receptor repertoire profiling in dogs
Metric | Mean | Median | Min | Max | Stdev | |
|---|---|---|---|---|---|---|
Cells | Estimated number of cells | 8,365.4 | 8,554.0 | 6,968 | 9,600 | 1,134.6 |
Fraction Reads in Cells | 1.0 | 1.0 | 95.9% | 96.9% | 0.4% | |
Mean Reads per Cell | 43,009.6 | 28,875.0 | 19,952 | 72,253 | 25,462.9 | |
Median Genes per Cell | 1,447.0 | 1,531.0 | 1,162 | 1,635 | 186.0 | |
Total Genes Detected | 14,549.2 | 14,610.0 | 14,090 | 14,751 | 268.6 | |
Median UMI Counts per Cell | 4,237.0 | 4,421.0 | 3,246 | 4,955 | 720.3 | |
Sequencing | Number of Reads | 337,945,537 | 267,296,412 | 191,543,369 | 514,405,307 | 158,561,283 |
Number of Short Reads Skipped | 0 | 0 | 0 | 0 | 0 | |
Valid Barcodes | 92.6% | 92.7% | 91.9% | 93.4% | 0.6% | |
Valid UMIs | 99.8% | 99.8% | 99.8% | 99.9% | 0.1% | |
Sequencing Saturation | 64.0% | 59.6% | 49.6% | 80.1% | 13.9% | |
Q30 Bases in Barcode | 89.3% | 90.0% | 87.9% | 90.1% | 1.1% | |
Q30 Bases in RNA Read 1 | 82.9% | 81.7% | 81.6% | 85.1% | 1.7% | |
Q30 Bases in RNA Read 2 | 85.3% | 85.3% | 84.9% | 85.8% | 0.4% | |
Q30 Bases in UMI | 88.9% | 89.4% | 87.8% | 89.7% | 0.8% | |
Mapping | Reads Mapped to Genome | 70.3% | 69.9% | 67.1% | 73.4% | 2.9% |
Reads Mapped Confidently to Genome | 67.9% | 67.6% | 65.0% | 71.0% | 2.6% | |
Reads Mapped Confidently to Intergenic Regions | 7.0% | 6.8% | 5.8% | 8.2% | 0.9% | |
Reads Mapped Confidently to Intronic Regions | 6.1% | 6.2% | 5.1% | 7.2% | 0.8% | |
Reads Mapped Confidently to Exonic Regions | 54.9% | 55.6% | 52.2% | 56.7% | 1.9% | |
Reads Mapped Confidently to Transcriptome | 47.8% | 47.2% | 45.9% | 50.6% | 1.7% | |
Reads Mapped Antisense to Gene | 2.3% | 2.2% | 2.1% | 2.6% | 0.2% |
