I recently inquired GISAID about their current criteri for SARS-CoV2 assembly submission in order to quantify the success rate of sequencing happening in our lab using MinIon and Artic v4.1 protocol. However, I am not convinced what they are try to explain here when they say longer than 100 nucleotides in the line

All sequences containing <50% Ns and that are longer than 100 nucleotides are released on EpiCoV.

Besides, I get warning for the genomes which have horizontal coverage >90% and end up with Warning tag when I screen my assemblies using CovSurver. I am not sure what should I make of it i.e. whether they are fit for submission or not. Is there a way to

Other than that I am confused regarding Variant selection to build Consensus sequence. Should I consider Variants with Variant Allele Frequency > 0.8 or all the variants (even low frequency and subclonal variants; PS for definition read COVIGATOR VAF classification criteria)?