Not able to detect iuc5 aerobactin allele type in updated version

[95aastha]

The updated version of v3.1.0 is not able to detect iuc5 allele type. The same data was previous analyzed using v2.3.0 and the genomes carried iuc5, but with the updated version, aerobactin locus alleles are detected, but iuc5 allele type is not annotated. Such a case occurs for all iuc5 allele type carrying genomes.

Kindly help me sort this issue.

[Marysteph]

Hi @95aastha, Could you please share with me a sample genome where the iuc5 allele is not detected? I will look into it. Thanks

[95aastha]

I have attached one of the genome file.
GCA_020830115.1_ASM2083011v1_genomic.txt

[Marysteph]

Thanks for sharing the data. The reason why AbST and iuc lineage are not annotated it's because we only report the virulence locus as present if at least half of the genes are detected (e.g. at least 3 of the 5 iuc locus). See the documentation

If <50% of the genes are detected, Kleborate reports the ST as 0 and the lineage as -. In your v2 output (AbST column), 61-3LV indicates a 3-locus variant of ST61 ( 2/5  loci match ST61).
GCA_020830115_kleborate_v2.txt
GCA_020830115_kleborate_v3_output.txt