Help interpreting results from ChroQueTas

[cimendes]

Hello! Thank you for the great tool!

I've been testing it with some Candidozyma auris data (assemblies generated from ONT), and I'm having trouble interpreting the Fungicide_resistance results. In particular, I'm having trouble interpreting the confidence. For example:

Protein	Fragment	Position_reference	AA_reference	AA_query	Fungicide_resistance
Cyp51	1	132	Y	F	5-fluorocytosine(NA/-8),Amphotericin_B(8/-8),Anidulafungin(NA/-8),Caspofungin(8/-8),Fluconazole(2/-8),Itraconazole(8/-8),Micafungin(NA/-8),Posaconazole(8/-8),Voriconazole(2/-8)

What does the NA stand for in (NA/-8)?
For example, what does (8/-8) mean?

Additionally, I have a sample with the exact same result, just different segments. What does the segment mean?

Protein	Fragment	Position_reference	AA_reference	AA_query	Fungicide_resistance
Cyp51	1	143	K	R	Fluconazole(2/NA),Voriconazole(2/NA)
Cyp51	2	143	K	R	Fluconazole(2/NA),Voriconazole(2/NA)
Tac1	1	640	A	V	Fluconazole(1/NA)

Thank you for your help!!!

[nmquijada]

Hi @cimendes

Thanks a lot!

The confidence scores are the values we are using to label the fAMR mutations under a certain level of experimental evidence. You can find more info in this section of the wiki and in the latest preprint.
So, the output from each antifungal in ChroQueTas will have 2 numbers between brackets divided by an /. The number on the left side (positive) is the strongest level of evidence overall accounting all entries from FungARM database that supports that the mutation to cause fAMR. The number on the right side (negative) is the strongest level of evidence that supports that the mutation does not cause fAMR.

So, in you example Fluconazole(2/NA), this means that the mutation Cyp51 K143R has a positve confidence score of 2, which means that "the mutation was created in the same gene but expressed in another species with potentially non endogenous level of expression and effect on resistance was confirmed by experimental measurements". On the other hand, the NA for the "negative scores" that "no evidences for the mutation not causing fAMR have been reported". All in all, for your example this means that the scientific evidences support strongly that Cyp51 K143R is associated with fluconazole resistance in C. auris.

Fragments mean the number of times that the protein was found your genome. Having 2 fragments means that it was found in 2 different positions in your genome, either by potential duplications, aneuploidy or if your genome is too fragmented (you can adjust the value for --min_cov. The highest, the better). You might have to inspect the .paf and .blastp.txt for Cyp51 if you would like to dig deeper in the possible reason.

Thank you very much for your comment. I would use this to improve the documentation for the next release, as I think the users would appreciated it.

N

[cimendes]

Thank you so much @nmquijada for your very thorough reply! We've been evaluating your amazing tool to add to our TheiaEuk workflow (if you're curious, the paper describing it is here). This workflow is mainly designed to be run on the Terra.bio platform! We'll be adding extensive documentation describing ChroQueTas (great name by the way!) so I'm happy to contribute in any way that I can! :D

Thank you so much for making AMR determination on fungal genomes accessible!