waxsys.tree.df: waxsys.tree.df

In ababaian/palmid: Viral RNA Dependent RNA Polymerase Analysis Suite

waxsys.tree.df

Description

Waxsystermes Virus example data. A merged waxsys.pro.df file and waxsys.tree.phy to have cleaned-up labels for plotting on a tree#'

Usage

data(waxsys.tree.df)

Format

data.frame with 4159 obs. of 13 variables

Details

#'

• qseqid. Query or input sequence name ("SRR9968562_waxsystermes_virus_microassembly")

• qstart. Coordinate of alignment start, 1 based

• qend. Coordinate of alignment end, 1 based

• qlen. Length of aligned sequence on query

• sseqid. Subject (palmDB) sequence identifier, sOTU used.

• sstart. Coordinate of alignment start, 1 based

• send. Coordinate of alignment end, 1 based

• slen. Length of aligned sequence on query

• pident. Percent AA-identity between query and subject. (0–100)

• evalue. Expectance value for alignment

• cigar. CIGAR alignment string for query alignment

• full_sseq. Complete subject sequence (including non-aligned)

• tspe. Taxonomic species of the palmDB match if available, else "."

• tfam. Taxonomic family of the palmDB match if available, else "."

• tphy. Taxonomic phylum of the palmDB match if available, else "."

• gbid. Percent identity mapped to closest GenBank record

• gbacc. Accession of closest GenBank record.

Source

Waxsystermes Virus Tutorial

ababaian/palmid documentation built on July 1, 2023, 1:09 a.m.