Genetic diversity across the SARS-CoV-2 genome
The scatter plots describe a sliding window analysis (100 nt windows with 50 nt of overlap; regions with multiple gaps not considered)
of the following measures of sequence conservation for
Alig02 multiple sequence alignment used in the database:
-PIS: percentage of identical sites
-PPI: percentage of pairwise identity
Alignment info
Alig02
All human SARS-CoV-2 complete genomes with high coverage from the GISAID initiative (www.gisaid.org/),
downloaded at 18-03-2020. The multiple sequence alignment was performed using the default parameters of the MAFFT webserver (https://mafft.cbrc.jp/alignment/server/).
Define below a window to see on the multiple sequence alignment:
or use a window midpoint (roll over a dot on the graph) to visualize the corresponding section of the alignment
Click and drag on the graphs to zoom in
List of the most conserved genomic regions considering the PIS (100 nt windows):
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List of the most conserved genomic regions considering the PPI (100 nt windows):
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