Discrepant results between similar Salamae genomes

[flashton2003]

Hello,

We've isolated some subsp salamaes for one of our projects. I have a few questions about the SISTR output for these isolates:

sample	cgmlst_found_loci	cgmlst_matching_alleles	cgmlst_subspecies	o_antigen	serogroup	serovar	serovar_antigen	serovar_cgmlst	O antigen prediction	H1 antigen prediction(fliC)	H2 antigen prediction(fljB)	Predicted identification	Predicted antigenic profile	Predicted serotype	average_depth	snp_count	indel_count	N_count	reads_cov	Reference	Organism from Esmie	Salmonella genus
CQJ13L	330	129	salamae	-	B	II 1,4,12,[27]:a:z39|II 4:a:z39	II 1,4,12,[27]:a:z39|II 4:a:z39	II 1,4,[5],12,[27]:b:[e,n,x]	4	a	z39	Salmonella enterica subspecies salamae (subspecies II)	4:a:z39	II [1],4,12,[27]:a:z39	70.3072	40928	0	0	89.86	GCF_019339485.1		Salmonella species
CQJ127	330	134	salamae	-	B	II B:-:e,n,x	II B:-:e,n,x	II 1,4,[5],12,[27]:b:[e,n,x]	4	z	e,n,x	Salmonella enterica subspecies salamae (subspecies II)	4:z:e,n,x	II [1],4,12,27:z:e,n,x	62.4964	40202	0	0	89.21	GCF_019339485.1	Salmonella Typhimurium	Salmonella typhimurium

1. Neither of these samples have a prediction in the o_antigen column, but when I blast them against your database, they have quite a good match (97% similarity, >99% coverage) to "304|584|1,4,12,27|B" from the wzx database. Is this match not good enough to call the O antigen? Or is there uncertainty about record 304?
2. They are quite similar results across most fields (and for my blast results against the wxy and wxz databases), but they have different results in the output. How come?

Here are the fasta files, in case you want to dig in.

https://www.dropbox.com/scl/fi/ppkiflqyvtwrn28nah9s6/CQJ127_S25_L001.fna?rlkey=t19wktth1uguutnmqkuej3jq7&dl=0 https://www.dropbox.com/scl/fi/k4yg4iwo1k0mjdinyahx0/CQJ13L_S23_L001.fna?rlkey=woawgupve273z3b7y7tx2xipi&dl=0

Thanks,

Phil