Table 1 Overview of the mapping parameters for the 10x Genomics scATAC-seq datasets established in mice skins.
From: Single-cell chromatin landscapes of mouse skin development
| Â | E13.5 | E16.5 | P0 |
|---|---|---|---|
Estimated number of cells | 8016 | 7714 | 7896 |
Median fragments per cell | 19906 | 27044 | 24006 |
Fraction of fragments overlapping any targeted region | 69.3% | 69.9% | 74.9% |
Fraction of transposition events in peaks in cell barcodes | 50.8% | 52.5% | 66.1% |
Fraction of read pairs with a valid barcode | 75.7% | 98.4% | 97.8% |
Q30 bases in Read 1 | 91.4% | 94.3% | 91.8% |
Q30 bases in Read 2 | 90.8% | 93.8% | 91.2% |
Q30 bases in Barcode | 86.5% | 90.3% | 86.7% |
Q30 bases in Sample Index | 90.1% | 93.1% | 90.9% |
Enrichment score of transcription start sites | 8.13 | 8.15 | 7.31 |
Fraction of fragments overlapping TSS | 31.6% | 29.9% | 34.0% |
Fraction of fragments overlapping called peaks | 53.4% | 55.5% | 68.5% |
Fraction of transposition events in peaks in cell barcodes | 50.8% | 52.5% | 66.1% |
Fraction of fragments overlapping any targeted region | 69.3% | 69.9% | 74.9% |
Fraction of total read pairs mapped confidently to genome (>30 mapq) | 66.7% | 86.7% | 88.6% |
Fraction of total read pairs that are unmapped and in cell barcodes | 1.0% | 1.1% | 1.3% |
Fraction of total read pairs in mitochondria and in cell barcodes | 0.4% | 1.2% | 0.2% |
