Table 1.
SNV calling in single cells (<1973–2018)
| I cells | E cells | |||||
|---|---|---|---|---|---|---|
| I cell 1 | I cell 2 | I cell 3 | E cell 1 | E cell 2 | E cell 3 | |
| # Mapped reads (million)a | 267.10 | 323.26 | 357.83 | 204.68 | 82.67 | 123.79 |
| % Mapped readsa | 69.06 | 79.93 | 80.00 | 63.14 | 14.89 | 37.06 |
| Whole genome | ||||||
| # Covered bases (million)b | 67.79 | 74.15 | 105.54 | 102.06 | 22.49 | 52.69 |
| # Mutations | 11,098 | 12,551 | 19,729 | 1855 | 450 | 943 |
| Mutations per base | 1.64 × 10−4 | 1.69 × 10−4 | 1.87 × 10−4 | 1.82 × 10−5 | 2.00 × 10−5 | 1.79 × 10−5 |
| Mutation rate per cell division | 1.15 × 10−8 | 1.18 × 10−8 | 1.31 × 10−8 | 3.95 × 10−9 | 4.35 × 10−9 | 3.89 × 10−9 |
| Coding sequence | ||||||
| # Covered bases (million)b | 4.37 | 4.689 | 6.45 | 6.20 | 1.41 | 2.86 |
| # Mutations | 633 | 645 | 1.007 | 73 | 26 | 50 |
| Mutations per base | 1.45 × 10−4 | 1.38 × 10−4 | 1.56 × 10−4 | 1.18 × 10−5 | 1.85 × 10−5 | 1.75 × 10−5 |
| Mutation rate per cell division | 1.01 × 10−8 | 9.63 × 10−9 | 1.09 × 10−8 | 2.56 × 10−9 | 4.01 × 10−9 | 3.79 × 10−9 |
| Validation | ||||||
| MAPD score | 0.783 | 0.934 | 0.696 | 0.687 | 1.269 | 1.124 |
| % Single-cell artifact signaturesc | 1.3 | 1.3 | 1.8 | 2.5 | 3.5 | 2.9 |
-
aUniquely mapping reads after removal of duplicates; lower on average read numbers of E cells versus I cells were caused by overall different outputs of the respective sequencing runs.
-
b(Coverage ≥20, both in the single-cell examined and the merged mapping result of the single cells of the opposite stem cell lineage.
-
cCombined SBS scE and SBS scF fractions (Petljak et al. 2019).
