Dear @A-N-Other @nathanhaigh,

I am not getting SNPs for a sequence compared to a reference, could it be because the identity b/w these two sequences is (79%). I am using a multi-FASTA file. For most of the sequences, I am generating SNPs for only the initial part (while using MAFFT, I am able to see there are SNPs in the later part as well). For others, it is able to generate the sequences for the terminal region, but the middle region is mostly missing.

I am not able to understand why this would happen.

I used the following commands:

nucmer --forward -p output $ref $input
show-coords -r -c -l output.delta > output.coords
show-snps output.delta -T -l > output.snps

Pls help me.

Best,
Ankeet