How to look up gene names using SNP locations on Practical Haplotype Graph

Question

[Dylan]

Hello!

I am new to studying maize genomics and would like to map a dataset of mutations to gene names.

The dataset is from Genomes2Fields, where for each sample we get an identifier for the maize type (e.g. 2369/DK3IIH6) and whether or not there was a mutation at a specific location (e.g. S1_162464).

My question is, how do I find the gene name on which a mutation, e.g. S1_162464 finds itself?

I have been looking through the PHG and rPHG for hours now and am still confused.

Any help would be greatly appreciated. Thank you in advance!

Answer 1

[pjb39]

Because the PHG does not store gene names, you will not be able to use it to find them. Instead, you could use another tool like the B73 genome browser at maizegdb.org.

[Dylan]

Ah I see, thank you pjb39!