Characterization of C1 single-cell WGA artifacts.

<p><b>(A)</b> The spectrum of base changes at ADO sites. Plotted is the mean percentage of ADO sites accounted for by each of the four bases across all CRL2338/HCC1954 (red, n = 50) and CRL2339/HCC1954BL (green, n = 49) cells. (<b>B)</b> The genomic distribution of ADO sites. Shown is the mean percentage of ADO sites on each chromosome compared to the expected distribution, assuming equal distribution of ADO sites across the genome (random, black) for CRL2338/HCC1954 (red, n = 50) and CRL2339/HCC1954BL (green, n = 49) cells. The random distribution is generated by equally distributing ADO sites across chromosomes based on the size of the targeted regions on each chromosome. (<b>C)</b> The spectrum of bases changes at false SNVs. Shown is the mean percentage of each possible base pair change at false SNVs identified in CRL2338/HCC1954 (red, n = 50) and CRL2339/HCC1954BL (green, n = 49). (<b>D)</b> The genomic distribution of false SNVs. Shown is the mean percentage of false SNVs on each chromosome compared to the expected distribution, assuming equal distribution of false SNVs across the genome (random, black) for CRL2338/HCC1954 (red, n = 50) and CRL2339/HCC1954BL (green, n = 49) cells. The random distribution is generated by equally distributing false SNVs across chromosomes based on the size of the targeted regions on each chromosome. (<b>E)</b> Comparison of the variant allele frequencies in bulk genomic to DNA to single-cell ensemble variant allele frequencies in CRL2338/HCC1954. Note that CRL2338/HCC1954 cells are near tetraploid by karyotype, which is expected to lead to VAFs ranging from 0.25–0.74 for heterozygous loci. (<b>F)</b> Comparison of the variant allele frequencies in bulk genomic to DNA to single-cell ensemble variant allele frequencies in normal diploid CRL2339/HCC1954BL cells.