sampleGenomePileup {ProActive} | R Documentation |
sampleGenomePileup
Description
A pileup file generated during read mapping to the *Salmonella enterica* LT2 genome. Report...
Usage
sampleGenomePileup
Format
## 'sampleGenomePileup' A data frame with 48,575 rows and 4 columns:
- V1
Accession
- V2
Mapped read coverage averaged over a 100 bp window size
- V3
Starting position (bp) of each 100 bp window. Starts from 100.
- V4
Starting position (bp) of each 100 bp window. Starts from 0.
Details
This dataset was generated by extracting DNA from a culture of *Salmonella enterica* LT2 (LT2) infected with phage P22. The DNA was shotgun sequenced with Illumina (paired-end mode, 150 bp reads). The sequencing reads were mapped to the LT2 reference genome (NCBI RefSeq NC_003197.2). The bbmap.sh bincov parameter with covbinsize=100 was used to create a pileup file with 100 bp windows.
Source
<https://pubmed.ncbi.nlm.nih.gov/25608871/>