intraHostVariants: SNVs from multiple organs of individuals with postmortem...

In MetaEntropy: Functional Shannon Entropy for Virome Mutational Analysis

SNVs from multiple organs of individuals with postmortem SARS-CoV-2 detection

Description

SNVs were inferred from Illumina (2 x 150) sequences. Reads were aligned to the Wuhan-Hu-1 reference genome (MN908947.3) with BWA, followed by variant calling using LoFreq with source quality correction. The VCF file was post-processed with BCFtools to prevent reference and strand biases and remove positions supported by fewer than 1,000 reads.

Usage

intraHostVariants

Format

A data frame with 213 rows and 16 columns.

Source

Manrique, J. M., Maffia-Bizzozero, S., Delpino, M. V., Quarleri, J., & Jones, L. R. (2024). Multi-Organ Spread and Intra-Host Diversity of SARS-CoV-2 Support Viral Persistence, Adaptation, and a Mechanism That Increases Evolvability. Journal of Medical Virology, 96(12), e70107. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/jmv.70107")}

See Also

See vignette("intraHostVariants", package = "MetaEntropy") for a step-by-step tutorial on analyzing this dataset.

MetaEntropy documentation built on Sept. 3, 2026, 5:10 p.m.