What do lower-case bases mean?

[Noma-M]

Hi

Thank you for creating this great platform to investigate and visualize STRs. I need help with further interpreting and understanding EH results on GraphAlignmentViewer. Maybe I’ve missed this and it has been posted elsewhere, but wanted to know what do the lower-case nucleotides indicate in GraphAlignmentViewer. For instance, in the example that is provided on the GraphAlignmentViewer github page, there are some bases in alignments that are lower-case: (https://github.com/Illumina/GraphAlignmentViewer)

Would this indicate soft-clipped bases (which are different from SNPs)?

[uguenke]

Hi,

It represents low quality bases (i.e. Q<20). You can find information in the paper published by Ibanez et al. (DOI: 10.1016/S1474-4422(21)00462-2 ), especially in supp data. They give examples of different genotypes and tricks to interpret the results.

[Noma-M]

Thanks @uguenke. This helps a lot