Extended Data Fig. 4: Distribution of polymorphic sites along three selected genomes.
From: Long-term stability and Red Queen-like strain dynamics in marine viruses
The three longest T4-like genome fragments were chosen (ranked 9433rd, 10382nd and 13113rd) because T4-likes are the most extensively studied group and have the best annotations. Each diagram shows all predicted open reading frames and their sense direction as depicted by an arrow. The y-axis on the left side (for thin black bars) shows the number of months that each location exhibited a SNP. The position along the x axis corresponds to their position along the genome. Y axis on the right (red line) shows the average number of SNPs per basepair on a 500 bp moving average. Note that only about ~5% of the sites are polymorphic although this is hard to visualize. For details, please refer to annotations and the per gene density of 20 representative (including the ones shown here) T4-like viruses is included in Supplementary Tables under the tab “SNPsAmongT4LikeViruses” Although not selected for this reason, these three show strikingly different patterns in SNP distributions, from relatively uniform (top panel) to very patchy with a few hotspots (bottom panel). Note y axes are scaled for each panel, and the top and middle ones have similar SNP densities to each other over most of their lengths.
