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
You need to change your code. It is not alphabet frequency. It is consensus matrix. Example code and image below:

    library(Biostrings)
    fastq <- readDNAStringSet("sample.fastq","fastq")
    ## At each position, base frequency
    afmc=consensusMatrix(fastq, baseOnly=T,as.prob = T)
    tafmc=t(afmc)
    matplot(tafmc[,-5], type="l", lwd=2, xlab="Read Length", ylab= "Base frequency at each position")
    legend(legend = colnames(tafmc)[-5],"topright",col=1:4, lty=1:4, lwd=2)

<a href="https://ibb.co/koRDVG"><img src="https://preview.ibb.co/cykU4b/test.png" alt="test" border="0"></a>

5th column is others (other than A,T, G and C). 