bac.f: Example dataset for bacsnp

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

Example dataset for bacsnp

Description

A dataset containing SNP frequency data for demonstration purposes. This dataset represents a small subset of SNPs with coverage and alternative allele frequency information.

Usage

bac.f

Format

A data frame with 6 rows and 19 variables:

CHROM

Chromosome or reference identifier (character).

POS

Position of the SNP on the chromosome (integer).

ID

Unused identifier; typically NA (character).

REF

Reference nucleotide (character).

ALT

Alternative nucleotide(s), separated by commas (character).

QUAL

Quality score of the SNP (character).

FILTER

Filter status; typically NA (character).

INFO

Additional information about the SNP, such as coverage and allele counts (character).

GT

Genotype of the SNP (character).

PL

Phred-scaled likelihoods for genotypes (character).

DP

Total coverage at the SNP position (character).

DPR

Per-sample depth for each allele, separated by commas (character).

GQ

Genotype quality (character).

ISO

Isolate identifier (character).

COV

Total coverage at the SNP position (numeric).

COV.REF

Coverage of the reference nucleotide (numeric).

COV.ALT1

Coverage of the first alternative nucleotide (numeric).

REL.REF

Relative frequency of the reference nucleotide (numeric).

REL.ALT1

Relative frequency of the first alternative nucleotide (numeric).

Examples

data(bac.f)
head(bac.f)

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