mummer -maxmatch -n -l 100 ratg13.fasta prC31.fasta > ratg13-prc31.mumm
mummer -maxmatch -n -l 50 cov-fasta/ncbi-ref.fasta cov-fasta/ratg13.fasta > output/ncbiref-ratg13-09091457.mumm
mummerplot output/ncbiref-ratg13-09091457.mumm
mummerplot -x "[0,32000]" -y "[0,32000]" --png output/ncbiref-ratg13-09091457.mumm
JC Question: Do mutation hotspots cover spike and Mpro regions?
Based on NCBI NC045512:
S gene is 21563 - 25384, which contain a large gap.
3CL nsp5Ais 10055 - 10972. The maxmatch results are:
ratg wuhan
9227 9339 57
10487 10615 77
10661 10791 63
So, the beginning and middle sections of 3CL are mutation hotspots too.
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