variants: Variant data

In jtmccr1/HIVEr: Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

Description

And example of the iSNV data that comes out of the variant_calling_pipeline.

Usage

variants

Format

a data frame with 24 rows and 33 variables.

Id

The Id of the indexed sample for sequencing - can be multiple Id/ SPECID

MapQ

The average MapQ of reads with the variant

Phred

The average Phred of the variant base

Read_pos

The average position of the variant base on the read

chr

Chromosome - genomic segment

cov.ctrl.bw

The coverage of the plasmid control at the position in the reverse read

cov.ctrl.fw

The coverage of the plasmid control at the position in the forward read

cov.tst.bw

The coverage of the sample at the position in the reverse read

cov.ctrl.fw

The coverage of the sample at the position in the forward read

freq.var

Frequency of the variant

mutation

mutation as chr_refPosVar

n.ctrl.bw

The number of variant bases in the plasmid control in the reverse read

n.ctrl.fw

The number of variant bases in the plasmid control in the forwad read

n.tst.bw

The number of variant bases in the sample in the reverse read

n.ctrl.fw

The number of variant bases in sample in the forward read

p.val

DeepSNV p.val

pos

position on genomic segment

raw.p.val

Uncorrected deepSNV p.val

ref

nucleotide in the plasmid control

sigma2.freq.var

Estimated variance of frequency measurement

var

nucleotide in the sample

run

The sequencing run the sample was on

OR

A list of the open reading frames overlapping this position

coding_pos

A list of the positions relative to the start of the in the ORs

Ref_AA

Reference amino acid - either sample or plasmid consensus depending on pipeline variables

AA_pos

Codon of the ORs - a list

Var_AA

Variant amino acid

Class

List of variant classifications in each relative OR

LAURING_ID

Sample ID used in processing - akin to SPECID

dup

Sequencing sample duplicate - if applicable

coverage

Total coverage at this position

concat.pos

Position in concatenated genome - segments in the order used in alignment fasta file

gc_ul

genome copy/ul of sample

@source data-raw/variants.R

jtmccr1/HIVEr documentation built on May 29, 2019, 1:50 a.m.