parsed samtools pileup result excerpt

Description

parsed samtools pileup result excerpt – only locations where the called base differs from the reference

Usage

data(pup240_disc)

Format

A data frame with 31243 observations on the following 5 variables.

loc

location

ref

reference base

indiv

call for NA19240

depth

coverage depth at this base

pileup

pileup

Details

asterisks are to denote deletions...

Examples

data(pup240_disc)
pup240_disc[1:4,]

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ind1KG)
Loading required package: chopsticks
Loading required package: survival
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ind1KG/pup240_disc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pup240_disc
> ### Title: parsed samtools pileup result excerpt
> ### Aliases: pup240_disc
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(pup240_disc)
> pup240_disc[1:4,]
        loc ref indiv depth pileup
7961  12961   C     G     4      g
9074  14074   G     T     4     T$
11171 16172   C     A     2  ,$.$a
23462 28466   A     C     6     C,
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>