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SeqSero2
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O:9 interpretation #15

Closed ATML-TD closed 3 years ago

ATML-TD commented 5 years ago

Hello,

Most of my Enteritidis genomes are identified as Hillingdon due to detection of the O-9,46_wbaV__1002 sequence with no apparent link to the match score, , e.g.:

Output_directory: SeqSero_result_08_26_2019_12_42_017562833 Input files: Salm201905696_S134_R1.fastq.gz O antigen prediction: 9,46 H1 antigen prediction(fliC): g,m H2 antigen prediction(fljB): - Predicted subspecies: I Predicted antigenic profile: 9,46:g,m:- Predicted serotype: Hillingdon associated log: O_scores: O-1,3,19_not_in_3,10130 73.07692307692307 O-9,46_wbaV__1002 54.09836065573771 Special_scores: uniqmers_I 100.0 gntR-family-regulatory-protein_dt-positive291 100.0 gntR-family-regulatory-protein_dt-negative291 89.81132075471699 allmers 12.978168162433965 sdf_I_AF370707333 91.20521172638436 sdf-I_AF370707__333 91.20521172638436

##other genome Output_directory: SeqSero_result_08_26_2019_12_42_014760921 Input files: Salm201905700_S136_R1.fastq.gz O antigen prediction: 9 H1 antigen prediction(fliC): g,m H2 antigen prediction(fljB): - Predicted subspecies: I Predicted antigenic profile: 9:g,m:- Predicted serotype: Enteritidis Note: sdf gene detected. associated log: O_scores: O-1,3,19_not_in_3,10130 73.07692307692307 O-9,46_wbaV__1002 80.84016393442623 Special_scores: uniqmers_I 100.0 gntR-family-regulatory-protein_dt-positive291 96.98113207547169 gntR-family-regulatory-protein_dt-negative291 86.79245283018868 allmers 13.15002227738527 sdf_I_AF370707333 91.20521172638436 sdf-I_AF370707__333 91.20521172638436

I dont really get how the O:9 is determined. Thx for your help

LSTUGA commented 5 years ago

Hey,

Thanks for asking. SeqSero2 uses the gene O-9,46_wbaV__1002 to differenticate O:9,46 and O:9. For genome Salm201905696, the match score of O-9,46_wbaV__1002 is too low to be called (default minimum match score is 70), which would influence the final prediction output. The low match score of the gene wbaV could be caused by unsufficient sequencing coverage; or, it's also possible that the wbaV in your Enteritidis genomes is a new allele that differs from the one in our allele database. You can share your genomes to us and we will be happy to do the troubleshooting and try to fix the issue.

Thanks!