Using your mouse, you can make regional selections through the panel at the bottom of the inspection screen. Through this section you can make more precise selections by explicitly defining a range, and can get sequences for the selected region or for the entire split.
GC content may explain some variation in coverage (more info on wavy coverage patterns). Using this section you can overlay GC content signal on your mapping results. The GC content of the reference sequence calculated as the moving average of a 'sliding window' sampled every 'step size'.
Sliding window size (nt): | |
Step size: | |
Color: |
The y-axis on the left-hand side of each plot is automatically scaled per sample as a function of the maximum coverage value. Using this section you can change the y-axis maximum for each sample independently, or set a single value for all samples to make coverages more comparable.
Show or hide single-nucleotide variant information and/or insertion/deletions anvi'o identified during the profiling of read recruitment. IN/DELs reaching the specified min sequence length will be marked in red.
By default, the y-axis on the right-hand side of each plot is set to a fixed scale of 0-1, but if the corresponding box is unchecked, the y-axis maximum will be set independently for each sample as the max of (1) max variability of SNVs, or (2) max count/coverage value of IN/DELs in the sample.
See this for more information on how to study microbial population genetics in anvi'o beyond displaying them in the context of reference sequences.
Show SNVs | |
Show IN/DELs | |
SNV bars from bottom | |
Scale direction upwards | |
Fixed y-scale |
Mark IN/DELs greater than sequence length: |
If you zoom in enough on a region, nucleotide and codon information will appear at the bottom of your screen when applicable. Here you can toggle that feature and/or disable vertical lines that highlight the position of your mouse on the screen.
Show nucleotides for selected sequence | |
Show vertical mouse-over highlight box |
Change colors of genes based on their functional annotations. You can also manually color genes temporarily. First, righ-click on a gene. It will add the gene into the list below with a default color. Then, you can use the color picker next to it to set a color manually. To see the effect of changing colors, you need to press the 'Redraw Gene Arrows' button.
Color |
Category |