waxsys.palm.sra: waxsys.palm.sra

In palmid: RdRP Analysis Suite

Description

Waxsystermes Virus example data. Sequencing libraries in the Sequence Read Archive (SRA) for which Waxsys or related viruses have been identified in the Serratus Database. Including associated sequencing library meta-data.

Usage

data(waxsys.palm.sra)

Format

data.frame with 4159 obs. of 13 variables

Details

#'

• run_id. Sequencing library identifier in the SRA

• palm_id. PalmDB unique identifier for RdRP sequence in library

• coverage. Read coverage of contig containing RdRP

• sOTU. Species-like Operational Taxonomic Unit to which palm_id belong

• qseqid. Input query sequence name

• pident. Identity between input sequence and respective sOTU

• evalue. Expectence value for alignment

• sra_sequence. Matching sequence in the sequence library

• biosample_id. Corresponding identifier for the biosample database

• scientific_name. Provided organism meta-data

• date. Load date for sequencing library

• lng. Longitude meta-data (if available)

• lat. Latitude meta-data (if available)

Source

Waxsystermes Virus Tutorial

palmid documentation built on Oct. 15, 2021, 9:06 a.m.