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

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:


Start position: End Position:

or use a window midpoint (roll over a dot on the graph) to visualize the corresponding section of the alignment


Midpoint:

Click and drag on the graphs to zoom in

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