Synteny track popups contain additional information about the syntenic regions in both the "originating" species or assembly (i.e. the species or assembly whose JBrowse you are currently viewing—"originating" does not refer to phylogeny of the species), and the "target" species or assembly. In the example to the left, the originating species and assembly is rat RGSC v3.4; the target is human build v37. The information given in the popup includes:
Source: This is the name of the source file. For synteny tracks, the source is "synteny".
Class: Gives the species and assembly of the target.
Genome location: The full genomic position of the synteny block in the originating species/assembly, shown in the format Chr:Start..Stop. This value links to the JBrowse view of the entire syntenic region, which could be longer or shorter than the region currently displayed.
Feature length: The length in base pairs of the syntenic region in the originating species/assembly (in this case, rat v3.4).
Synteny Block ID: An arbitrary numerical value assigned to the synteny block in the target species/assembly which matches the syntenic region currently viewed.
Corresponding Synteny Block Location: The genomic position of the synteny block in the target species/assembly, shown in the format Chr:Start..Stop. This value links to the JBrowse version for the target species/assembly, showing the entire syntenic region in that species or assembly (opens in a new browser window or tab), facilitating comparisons between the syntenic regions in the two species/assemblies. The synteny tracks in that JBrowse view will also link back to this one.
Synteny Block Length: The length in base pairs of the syntenic region in the target species/assembly (in this case, human v37. The syntenic region in this example is human chromosome 2 between 71,305,636 and 71,411,293, having a length of approximately 110 Kb.). Note that the length of the synteny blocks in the two species are not the same size, possibly because of errors in the sequences, but more likely because the intergenic and intronic regions have been increased, reduced or both through speciation.