Understanding how MEGAN6 Compares Samples

I selected two Meganized DAA files to be compared.
If using relative abundances of each read, what does the heatmap in the left side bar indicate?
Does this indicate that there are more Proteobacteria in one sample compared to the other? Or is the heat map indicating the absolute abundance of reads within each sample (the number is just the count of reads within the samples?)

Both DAA files were analyzed with the SEED accession to seed database, however in the comparison file, only on sample ever shows up in the SEED window. Is MEGAN6 supposed to be able to compare samples based off of SEED’s functional groupings?


If you selected normalized counts during the comparison, the heatmap will show normalized counts, otherwise absolute counts.

MEGAN can compare functional classifications, too. Can you please check if the first sample, q7_blastx, actually has any SEED assignments and if they only disappear in comparison? It seems like something actually went wrong when assigning SEED classes in that samples, rather than being an issue of comparison.

The SEED assignments only disappear in comparison. They are present in both of the individual files.
It looks like MEGAN is putting all of the reads from both files into one big grouping instead of comparing the SEED groups against each other.

There are about 150,000 reads for each sample and the heatmap column on the right has a total of 300,000 reads