Raw fastq reads were adapter trimmed using Cutadapt v 1.1245, followed by quality trimming and quality filtering using the FASTX Toolkit (Hannon Lab, CSHL). Reads were paired up and aligned to the SARS-CoV-2 genome from isolate SARS-CoV-2/humanUSA/WA-CDC-WA1/2020 (MN985325.1) using Bowtie2 v 2.2.946. PCR duplicates were removed using Picard MarkDuplicates v 2.18.7 (Broad Institute). Variant detection was performed using GATK HaplotypeCaller v 4.1.2.047 with ploidy set to 2.

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