Fig. 4

Between-sample and within-sample variants of SARS-CoV-2 detected across methods. a SNVs detected between clinical samples against a reference genome (GISAID accession: EPI_ISL_402119) [27]. Alleles with ≥ 80% frequencies were called. *SNVs verified by Sanger sequencing. b Allele frequencies of the identified SNVs. Dark blue, amplicon; red, capture; grey, meta. Minor allele frequencies detected in serial dilutions of the cultured isolate (c) and clinical samples (d) across methods. Dark blue, amplicon vs meta; red, capture vs meta. Minor alleles are defined with ≥ 5% and < 50% frequencies. Besides general quality filter, iSNVs had to pass depth and strand bias filter as described in the “Methods” section