SARS-CoV-2 E484K mutation and del 69-70 deletion

[corneliusroemer]

I answered here:

NextClade Variant Calling info

Hi Katie! That’s a great question. There is no single answer for what proportion of the genome allows accurate variant calling. In general, the higher the coverage, the more confident/accurate the answer. It all depends on what you’re trying to achieve. If you give some more details about what you’re planning to do I will happily share some tailored advice. In general, as most of the important antigenic evolution happens in Spike, it’s very useful to cover Spike, in particular everything betw…

Why do you get low % genome recovery? Are you working with waste water and trying to generate a consensus from a waste water sequence? Or are you trying to be more cost-effective and only sequence parts of the genome of patient samples?