Additional file 2: of An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar Nathan Grubaugh Karthik Gangavarapu Joshua Quick Nathaniel Matteson Jaqueline Jesus Bradley Main Amanda Tan Lauren Paul Doug Brackney Saran Grewal Nikos Gurfield Koen Van Rompay Sharon Isern Scott Michael Lark Coffey Nicholas Loman Kristian Andersen 10.6084/m9.figshare.7563974.v1 https://springernature.figshare.com/articles/journal_contribution/Additional_file_2_of_An_amplicon-based_sequencing_framework_for_accurately_measuring_intrahost_virus_diversity_using_PrimalSeq_and_iVar/7563974 iSNV frequencies calculated using pseudo replicates (Figure S1.), sensitivity of measuring intrahost diversity at 5% (Figure S2.), metagenomic sequencing coverage depth (Figure S3.), and validation of iVar for intrahost single-nucleotide variant calling (Figure S4.), consensus calling (Figure S5.), and trimming (Figure S6.). (PDF 7109 kb) 2019-01-08 05:00:00 Viral sequencing Amplicon sequencing Intrahost evolution Zika West Nile SNP calling