The frequency of somatic SNVs per cell was estimated after normalizing genomic coveragefrequency of somatic SNVs per cell=# somatic SNVssurveyed genometotal size of genome

As the reads were aligned to the haploid reference genome, the frequency of somatic SNVs per base pair was calculated by dividing the frequency of somatic SNVs per cell by genome size and ploidy of the genome (ploidy = 2)frequency of somatic SNVs per base pair=frequency of somatic SNVs per celltotal size of genome*ploidy of genome

The surveyed genome per single cell/clone was calculated as the number of nucleotides with read mapping quality ≥20 and position coverage ≥20X.

For the LSC-differentiated hepatocyte comparison, the absolute de novo mutation frequencies were corrected for the number of cell divisions undergone since the zygote (table S2). We used 45.1 as the number of developmental mitoses (19) and assumed a subsequent turnover rate of one cell division per year, based on empirical evidence from rodents (49, 50). In total, 45.5, 46.3, and 61.6 cell divisions were estimated for both LSCs and differentiated hepatocytes from 5-month-old, 1-year-old, and 18-year-old individuals, respectively. For LSCs from 5-month-old, 1-year-old, and 18-year-old individuals, we then added, respectively, an estimated 33, 41.7, and 33 cell divisions during the enrichment process of stem cells, and 21.9, 24.5, and 21.9 cell divisions associated with clonal outgrowth of the single LSCs.

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