Closed danrlu closed 12 months ago
Correct, 8 of the contigs hit model Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin
.
For the rRNA gene variant model
the ORF_ID is named with the model and the query identifier .e.g., 3646_5918 | model_type_id: 40295 | pass_bit_score: 5300 | SNP: C2600T,A2145G,C2597T,A2045G,A2059G,C2611T | Neisseria gonorrhoeae 23S rRNA with mutation conferring resistance to azithromycin | QUERY: NODE_26_length_1251_cov_840.666388 NODE_26_length_1251_cov_840.666388
The Percentage Length of Reference Sequence
calculation is incorrect, which we will fix. Cheers.
We can't tell whether this is a bug or it is intended and it's us not interpreting the results properly.
Describe the bug/confusion
ORF_ID
is different and all other columns are identical, but the query contigs in theORF_ID
don't match theContig
column. I'm guessing this AMR hit was found in 8 different contigs, but wouldn't theContig
column show their corresponding contig names?Percentage Length of Reference Sequence
column, the number is -15.74 and < 0 (b/c the orientation of AMR gene and the contig are the opposite direction). This is the only time I see this column < 0 in all RGI outputs so wondering whether this is intended.Input
rgi main -i contigs.fasta -o contig_amr_report -t contig -a BLAST --include_nudge --clean
Input file https://github.com/danrlu/debug_data/tree/main/rgi
Error log No error.
CARD Version RGI version latest version of rgi CARD 3.2.6 (same result when uploading the contig.fasta to CARD website)
Thanks very much for this great tool and database and continuous improvements!!!
Originally noticed by @lvreynoso.