Hi,
please, how can I visualize nucelotides for every position. I have a percentage of bases but now I don't know how to create a plot.

    fastq <- readDNAStringSet("https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq","fastq")
    fastq
    freq <- alphabetFrequency(fastq, as.prob = T,baseOnly=T)

I would like something like this (sorry for quality):

![][1]


  [1]: https://image.ibb.co/cQPULG/base.png

    library(Biostrings)
    fastq <- readDNAStringSet("https://d28rh4a8wq0iu5.cloudfront.net/ads1/data/ERR037900_1.first1000.fastq","fastq")
    freq <- alphabetFrequency(fastq, as.prob = T,baseOnly=T)
    matplot(freq,type='l')
    legend(legend = colnames(freq),x=700,y=0.7,lty=1:5,col=1:5)

Note answer about consensusMatrix. That code is the best answer.
