ucsc genome browser variants read

Question

[khatami.mahshid]

hi all,

I have a question in UCSC genome browser. why in some reads the "C" variants is written on them but in others no?

this is the image

Answer 1

[Pierre Lindenbaum]

'C' is the alternative allele, the other reads have the reference allele 'T'

Answer 2

[H.Hasani]

If you also click on the bar bellow (pink and blue) you will retrieve the details of both alleles (see Variant Calls from High-Coverage Genome Sequence of an Archaic Denisovan Individual ), for example the allele frequency of both alleles is 50%.