bac.df: SNVs after BCF tool filtered MpileUp VCF data.

In wennj/bacsnp: Analyzing single nucleotide polymorphisms from baculovirus sequencing data

SNVs after BCF tool filtered MpileUp VCF data.

Description

A dataset containing the SNP positions and their nucleotide frequencies of three Illumina sequenced baculoviruses.

Usage

bac.df

Format

A data frame with 6 rows and 14 variables:

POS

Integer. Genomic position of the SNP.

QUAL

Numeric. Quality score of the SNP.

ISO

Factor. Isolate identifier (e.g., iIso1, iIso2).

GQ

Integer. Genotype quality score.

REF

Factor. Reference nucleotide.

ALT

Factor. Alternative nucleotides (up to three alternatives).

COV

Integer. Total coverage at the SNP position.

COV.REF

Integer. Coverage of the reference nucleotide.

COV.ALT1

Integer. Coverage of the first alternative nucleotide.

COV.ALT2

Integer. Coverage of the second alternative nucleotide.

COV.ALT3

Integer. Coverage of the third alternative nucleotide.

REL.REF

Numeric. Relative frequency of the reference nucleotide.

REL.ALT1

Numeric. Relative frequency of the first alternative nucleotide.

REL.ALT2

Numeric. Relative frequency of the second alternative nucleotide.

REL.ALT3

Numeric. Relative frequency of the third alternative nucleotide.

Details

A dataset containing SNP positions, quality scores, nucleotide frequencies, and relative frequencies for three alternative nucleotides across isolates of baculoviruses. The dataset provides information useful for SNP analysis, including reference and alternative coverage, as well as relative frequencies for each alternative nucleotide.

Examples

data(bac.df)
head(bac.df)

wennj/bacsnp documentation built on March 6, 2025, 2:12 a.m.