Root taxonomic assignment of reads that should be assigned proper taxonomic classification


I have some reads for a species capsid protein whose top hit is is being classified as root and not the capsid protein of that species and instead LCA skips over these assigns these reads the taxonomy of the second top hit. I have also provided the mapping files that is current ( but I am still not getting the proper taxonomy for those reads. Any help is appreciated.



Can you show me what that looks like in the inspector window


Thank you for the response. The species that I am referring to is panine betaherpesvirus 2. The reads under there have their first alignment assigned as root, although under that tab, you can tell that it should be human betaherpesvirus 5. Thus the alignment is skipped over the the next best alignment which is panine betaherpesvirus 2.