Contigs are arranged end-to-end along the X axis and the reference chromosomes are arranged bottom-to-top along the Y axis. Each pixel of the plot is colored according to how many short sequences of the corresponding contig have a match in the corresponding portion of the reference genome.
An identical assembly results in a diagonal line. A vertical gap in the plot might indicate a portion of the reference that is absent in the assembly, such as a plasmid, which is found in some bacteria populations.
|Y axis||X axis||Description|
|Reference||Assembly Position||A syntenic plot of assembled contigs compared to a reference. A reference genome must be specified in the sample sheet|