https://github.com/tseemann/snippy : "Rapid haploid variant calling and core genome alignment"

surely on some level - new to bioinformatics or not - you must understand 2 things:

1) it is not possible to answer your question based on this post, which provides essentially none of the details necessary

2) being rude to one of the most prolific moderators on this site will get you no where.

Dear Ujichu

I was wondering whether the quality of your third isolate is in tact! You could use --minqual threshold. It may also be likely that the reads covered at a particular window/site is less than 10, the default being 10.

Pl try checking the quality and proceed

Best prash