I want to know the genotypic difference (InDels and SNPs) between the Basmati and other Indian varieties so as to design markers. In this context, I started using the browser tool provided in the RIce Functional Genomics and Breeding database.I have encountered some problems which I request you to give solution for me.
1. The sequences of the deletions is not matching with the sequence of the reference genome.
2. I have deleted the reference sequence since I wanted to select the reference sequence fresh and start the analysis. However, after deleting the reference sequence I find that there is no way reference sequence can be loaded again.
Please tell me how to load the reference sequence in the browser and why there is the difference in the sequence of the deletion and that of the reference sequence.
Thank you for your information!
Sorry for my delay!
Yup. I also try your delete way of ref. It's true.
Anyway, our present ref is Nipponbare which was coded as CX140 in our accessions.