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Additional file 2: Fig. S1. Correlation of estimated alternative allele frequencies between metatranscriptomic and hybrid capture data. Fig. S2. Correlation of estimated minor alternative allele frequencies between biological replicates. Fig. S3. Correlation between sequencing depth and detected iSNVs. Fig. S4. Number of iSNV among three codon positions. Fig. S5. Haplotype frequency of proximal iSNVs within the gastrointestinal tract of patient P01.

Additional file 2: Fig. S1. Normalized coverage across SARS-CoV-2 genomes of serial dilutions of the cultured isolate sequenced by multiple approaches. Fig. S2. Sanger sequencing results of SNVs in clinical samples. Fig. S3. Box-plot of allele frequencies against SARS-CoV-2 genome copies per mL. Fig. S4. Taxonomy of clinical samples by unbiased metatranscriptomic sequencing. Table S2. Capture sequencing data summary of serial dilutions of the cultured isolate and eight SARS-CoV-2 positive clinical samples collected from Guangzhou (PE100). Table S3. Amplicon sequencing data summary of serial dilutions of the cultured isolate and eight SARS-CoV-2 positive clinical samples collected from Guangzhou (SE400). Table S4. Estimated minimum amount of sequencing data required to achieve ≥10X sequencing depth and ≥ 95% coverage for different methods. Table S5. Estimated minimum amount of sequencing data required to achieve high-confidence variants calling analyses for different methods. Table S6. Bioinformatic tools and parameters used in this study.