How reads differentiate O3,10 and O9,46

[alantsangmb]

I have two isolates analysed using reads:

isolate A:
check fastq id and make them in accordance with each other...please wait...
Final_Otype_list:
[('O-9,46_wzy', 20), ('O-3,10_not_in_1,3,19', 18), ('O-3,10_wzx', 5)]
$$$Genome: ST18000041_S26_L001_R1_trimmed.fastq
$$$No sdf exists
$$$Most possilble Otype: O-9,46

isolate B:
check fastq id and make them in accordance with each other...please wait...
Final_Otype_list:
[('O-3,10_wzx', 61), ('O-9,46_wzy', 56), ('O-3,10_not_in_1,3,19', 50)]
$$$Genome: ST18000012_S10_L001_R1_trimmed.fastq
$$$No sdf exists
$$$Most possilble Otype: O-3,10

Both isolate got hits to O-9,46_wzy, O-3,10_not_in_1,3,19 and 'O-3,10_wzx. I would like to ask how the algorithm choose the Otype between O3,10 and O9.46? The "O-3,10_KC688885_Anatum _rfb_complete_sequence" and "O-9,46_KC688887_Strasbourg_rfb_complete_sequence" in the database are highly similar. And isolate A is actually an O3,10 Salmonella by serotyping with sera.