Summary of results

Model name: typhi_v8, model date: 18/Dec/24

Sample	Amplicons by # of dominant unknown SNPs	Possible High Level Genotypes	Implied Genotypes	Implied AMR	Sequencing Reads	Mapped, correct length	Mapped, but too short/long
barcode1 S. Typhi negative wastewater	2, 0, 0, 0, 0, 0	-	-	-	32167	3015	820
barcode2 S. Typhi H58 + wastewater	11, 1, 0, 0, 0, 0	4	4.3.1.1 (94%)	gyrA_S83T (99%)	14187	2534	983

"-" fewer than 2 amplicons with 50 target organism reads and fewer than 2 SNPs

Classifier allowed soft clip (-s) of 25nt and 10nt length difference (-l) between reference and mapped read.

Report generated on 18/Dec/24 at 14:34. See models list

barcode1
S. Typhi negative wastewater

Back to Summary

Amplicon	Tot. Reads	Rejected on Length	% Target Org.	# Target Org.	All known SNPs	Dominant known SNPs	Dominant unknown SNPs	Implied Genotypes	Implied AMR
1_3_4.3.1	*	-	-	-	-	-	-	-	-
2.2.2_2	*	-	-	-	-	-	-	-	-
2.3.1_v12	*	-	-	-	-	-	-	-	-
2.3.2	2215	447	99.66%	1762	0	0	0
2.5_4.3.1.2.1_3.3	*	-	-	-	-	-	-	-	-
3.1.1_v5	*	-	-	-	-	-	-	-	-
3.3.1	*	-	-	-	-	-	-	-	-
4.3.1.1	*	-	-	-	-	-	-	-	-
4.3.1.1.P1_v2	*	-	-	-	-	-	-	-	-
4.3.1.2.1.1_4	*	-	-	-	-	-	-	-	-
4.3.1.2_v3	*	-	-	-	-	-	-	-	-
parC_v7	*	-	-	-	-	-	-	-	-
tviD_v2	*	-	-	-	-	-	-	-	-
acrB_v2	1463	311	99.83%	1150	0	0	0
gyrA	*	-	-	-	-	-	-	-	-
plasmid_ST6_C19241A^	*	-	-	-	-	-	-	-	-
chromosomal_MDR_cyaA	*	-	-	-	-	-	-	-	-
chromosomal_MDR_yidA	*	-	-	-	-	-	-	-	-
plasmid_MDR_AL513383.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029645.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029879.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029924.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029957.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_LT904879.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_LT904892.1	*	-	-	-	-	-	-	-	-

* Amplicon has fewer than 51 target organism reads

(?) Prediction is based on amplicon with fewer than 50 reads

^ Using model that was trained without negative cases - results are likely to be less reliable

barcode2
S. Typhi H58 + wastewater

Back to Summary

Amplicon	Tot. Reads	Rejected on Length	% Target Org.	# Target Org.	All known SNPs	Dominant known SNPs	Dominant unknown SNPs	Implied Genotypes	Implied AMR
1_3_4.3.1	143	65	100.00%	78	1	1	0	4.3.1 (96%)
2.2.2_2	212	112	100.00%	100	0	0	0
2.3.1_v12	191	50	100.00%	141	1	0	0	2.3.1 (18%)(?)
2.3.2	555	103	100.00%	452	0	0	0
2.5_4.3.1.2.1_3.3	326	111	99.53%	214	0	0	0
3.1.1_v5	*	-	-	-	-	-	-	-	-
3.3.1	150	37	99.12%	112	0	0	0
4.3.1.1	201	39	100.00%	162	1	1	0	4.3.1.1 (94%)
4.3.1.1.P1_v2	72	13	100.00%	59	0	0	0
4.3.1.2.1.1_4	433	186	99.19%	245	1	1	0	4 (99%)
4.3.1.2_v3	*	-	-	-	-	-	-	-	-
parC_v7	*	-	-	-	-	-	-	-	-
tviD_v2	392	92	99.33%	298	1	1	0	known, but uninformative allele (95%)
acrB_v2	605	93	99.61%	510	0	0	0
gyrA	157	64	100.00%	93	1	1	1		gyrA_S83T (99%)
plasmid_ST6_C19241A^	*	-	-	-	-	-	-	-	-
chromosomal_MDR_cyaA	*	-	-	-	-	-	-	-	-
chromosomal_MDR_yidA	*	-	-	-	-	-	-	-	-
plasmid_MDR_AL513383.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029645.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029879.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029924.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_CP029957.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_LT904879.1	*	-	-	-	-	-	-	-	-
plasmid_MDR_LT904892.1	*	-	-	-	-	-	-	-	-

* Amplicon has fewer than 51 target organism reads

(?) Prediction is based on amplicon with fewer than 50 reads

^ Using model that was trained without negative cases - results are likely to be less reliable

Consensus sequences

Sample	Amplicon	# of target reads	Consensus Mismatches vs Reference	Consensus sequence
barcode1 S. Typhi negative wastewater	1_3_4.3.1	0
barcode1 S. Typhi negative wastewater	2.2.2_2	0
barcode1 S. Typhi negative wastewater	2.3.1_v12	0
barcode1 S. Typhi negative wastewater	2.3.2	1762		ACGATAAACCGCTTCCGTCACCATCCCCGCCGGGTTAGTAAAGTTAATGACCCACGCATTCGGACATAATTCTTCAACATCCTTAATGATGTCAAAAATAACCGGAATGGTACGCAACCCTTTAAATAAACCGCCAGCGCCGTTGGTTTCTTGCCCCAGATAGCCGTGGCTAAGCGGGATACGCTCGTCCAGCTCACGGGCTTTGAGTTGACCAACGCGTAGCTGGGTAGTGACAAAATTAGCGCCTTTCAGCGCTTCCCGGCGATCCAGCGTTTTATACAATTTTAGCGGAACGCCTGCTTTATCAATCATTCGCTGGCAGAGATCATAAATAATGCCCAGCTTCTTTTTCCCGTCTTCAACGTCAACCAGCCATAATTCGGTGACAGGTAATTCATGGTAGCGCTTAATAAAGCCTTCAAGTAATTCAGGGGTGTAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATATCTCCCTTCAGTGTATGACACTGATATGTATTACGCTATGCCCGCTCGTAAGAAATAGCGTGACGTTCCCCGCGCTATTGGGGCAAGCGTGAAATGTAACTAATCGAGCAATGTAAACCGTTACTCATTAATTTCCGTCAATCGCTTCCGATAACTATTCGGCGTGAATGAGGTCATCTTCTTAAACGTTTTAATAAACAGACTTGGACTACTGTACCCGGC
barcode1 S. Typhi negative wastewater	2.5_4.3.1.2.1_3.3	0
barcode1 S. Typhi negative wastewater	3.1.1_v5	0
barcode1 S. Typhi negative wastewater	3.3.1	0
barcode1 S. Typhi negative wastewater	4.3.1.1	0
barcode1 S. Typhi negative wastewater	4.3.1.1.P1_v2	0
barcode1 S. Typhi negative wastewater	4.3.1.2.1.1_4	0
barcode1 S. Typhi negative wastewater	4.3.1.2_v3	0
barcode1 S. Typhi negative wastewater	parC_v7	16		TGGCACAATCACTAAACGCGTCGGGTTTTCGTGATCCGATTCATCGCGCAGGTCGTCCACCATCGGCAGTTTTTTATTGCGCATCTGCGCAGCAATCTGCTCCAGCACTTTTGCGCCAGATACCTGATGCGGTAACGCGGTGATCACCACGGCGCCGTCTTCTTTGGTCCATACCGCGCGCATACGCACGGAGCCACGCCCATTTTCGTAAATTTTACGAATTTCCGCACGAGGGATAATGATCTCCGCTTCGGTCGGGTAATCCGGCCCCTGGACGATATCCAGCAACTGATCCAGCGTCGTTTTCGGCTGCTCAATCAGCGTAATCGCCGCTTTCGCGACTTCGCGCAGGTTATGCGGCGGAATATCTGTTGCCATGCCCACCGCAATACCGGTGGTGCCGTTCAGCAGGATGTTCGGCAGACGCGCCGGTAACATTTTCGGTTCCTGCATGGTGCCGTCGAAGTTTGGCACCCAGTCCGCAGTCCCCTGACCGAGTTCGCTTAACAGCAGCTCGGCGTATTTGGACAGGCGGGATTCGGTATAACGCGTCGCCGCGAATGACTTCGGATCATCCGGCGCGCCCCAATTCCCCTGGCCATCGACCAGCGGGTAACGGTAAGAGAACGGCTGCGCCATCAGCACCATGGCTTCATAGCAGGCGCTGTCGCCATGCGGGTGATACTTACCCAGTACGTCG
barcode1 S. Typhi negative wastewater	tviD_v2	26		GCAAGCTGCTTAGTGATCGATAAGGTAATCTCACGTATTTGGTCCTGTTTCTCTTGTCGCCCCTCATCAAGATGATGATTAGTATTATTGATCACTCCCTTAAAAATAGCCGCAACGATCGCGTCACCAAACATATCGGTATAATGAGTAAGATCGTCGCCATTTTTTTCCAGGGCTCGTTTCTGCCCCCACTTTTCCATCAAATTTGTCGGGTTAACGCAGGGAATATCCATCCTGGCGGCGATGGTGTCGACATTTTTAATCAACCGACTACGGGATAGAATGACGGTTCCAGCACGAGTCACGGCATCAACATGTGTCATAAACATAACGCGATCGCGACCAAGAAGCTGAACGATTTCCATCATATCCTGTTCGATAGCATGCTCATCCATCTGCTCGACATTGATATTGCTTAATAAGGCACGATCGTCTTCCGACATTCCGGCAAAACAGGGATCGTCTTTGAGATAGGCCAGCAGTTTGTGTCGATTTCCTTGCGTGGCCAACGACCAGTACATGCACGCCCGCTCTGTTTGGCTAAAAAATTCATAGAAATGACGAGTTAAATAATTTATTTGTAAGCAGAACCCATAGGCCATAATCTTCTTCTGACTTGAAATCTCAATGATATAGAAATCAGAACGACTATGTACGTCGGTGTTTGAATAGTTTACATTAGGTCTAAAAATAAATGGTCGGACCTTTTCAGGAATGTCTATCAAGCCCAAAATAAACCGAATCTGCTGTAATGCCTCGCTGCTCGTATGCGTAAAACCATATATTCTCTTAAAGTTTGCCTGAAAATTAAAATAAGGC
barcode1 S. Typhi negative wastewater	acrB_v2	1150		CACAGGAAGACGACGATTAGCGAGATAGCATACAGGGCAGGGGCCTGGTTGCCGGACAACCGCTCCTGGTAGGACATCCCGGTCCAGTCATACCCAATGCCTGACGGCAGCTTGCTGGCCAGTTCTTCCATCATCGCCATCGCTTCACCAGTACTCTTGCCTGGCGCCGCCTGACCCAGAATTTCCATCGAAGGCAGACCGTTATAGCGTTCCAGACGCGGCGAACCATATTCCCAGCGGGAAGAGGAGAATGCGGAGAACGGCACCATCTGACCATCGCTACCACGAACGTACCAGTCGTTAATATCATCCGGCAACATGCGGTATTTCGCTTCGGACATCACGTAAACTTTCTTCACACGACCGCGATCGATAAAGTCGTTTACATAGCTGCCGCCCCATGCTGCGCCCAGCGTGGTATTAATGTCGCTAATAGACACGCCCAGCGCCTGAGCTTTTTCCTGGTCGATATCGATTTTAAACTGCGGCGTATCTTCCAGACCGTTAGGTCGAACGCCGACCAACAGATCAGGATATTTCGCCACCTCGCCGAACAACTGATTACGTGCCTGGGTGAGTTTTTCGTGACCAAGTCCCGCCTGGTCAATCAACTCGAAGTCAAACCCGGTTGCGGTGCCCAGTTCAACAATCGCCGGTAGGTTAAAGGCGAAGACCATCGCATCTTTAATTTGTGAAAACGCTGCGGTTGCCCGCTGGGTAATCGCTTCAACCTTGTTTTTTTCGCCTGGACGATCGGCCCAGTCTTTCAACGACACAAATGCAATACCGGTATTCTGACCGCGCCCTGCAAAACCGAAGCCGTTGACGGCGAATACCGATTCAACGTTGGCTTTCTCTTTGTTCAGATAGTAATCCGTGACCTCATCCAGCACTT
barcode1 S. Typhi negative wastewater	gyrA	0
barcode1 S. Typhi negative wastewater	plasmid_ST6_C19241A	0
barcode1 S. Typhi negative wastewater	chromosomal_MDR_cyaA	0
barcode1 S. Typhi negative wastewater	chromosomal_MDR_yidA	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_AL513383.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_CP029645.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_CP029879.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_CP029924.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_CP029957.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_LT904879.1	0
barcode1 S. Typhi negative wastewater	plasmid_MDR_LT904892.1	0
barcode2 S. Typhi H58 + wastewater	1_3_4.3.1	78	Pos:1655 (96%) , Change:A>G, Implication: 4.3.1	CGATGGTACTGAACAACCCTTTCGCATGCTTTTCACCGACGAGCGGTACCAGCGTGGAGCTGGGGCGGATGACATCCATCTTGCGTACAAAGAAGAAGTAGGCGAAGGCCACGGAAAGGAAGCTATAGGTTGCCCACGGTAGCGGCCCCCAGTGGAACAGGCTGTACGCCAGGCCTATCTCTTTCGCGCCCGTGGAATTGGGTTCCAGGCCGAACGGCGGGGTGGAGATATAGTAGTAGATCTCAATAGAGCCCCAGAACAGAACCGCAGCGGATGTACAGGAGGCGAACATCATGAAAATCCAGCTGGCGGTGCTAAACTCCGGTTTTTCGTCACCTAATCTCTTTTTGGCATAGGGGCCAAAAACCAGCCAGAACCAGCTGAAGAGCATGACGACCATATACCATTCAAATGCCCAACCCCAGACGTTGGTGACATAACTGAATACCGCATTAATAACGACGTTAGCGGCATCAAGATCTCTGACTGTTAGCCAGCAAAGTATCCCGACAATTATTAATAGCGGAAAAAAAACCTTCGGTTCAATTCCCGATTTTCTCTTTTCATTTTTCATAAGTGAATTCCAGTGTGAAAACGAAATTTATTTAGCGTGCCAGTTCATGAACGTTTGTTTATTTATTATTAATGATTTGTTGATAAGTTTTTAACCTCTGGGACGCCTCAATGAGTAACTCATAATGGGTATTCATTTCGGGTGATTCTGTTATCTGTGTCACACTTTTTTGCGTTGATTATTTTGTGTTTAAATTTTGATTTTTTCTTTATTTATCAATCTGTTGGTTGTGGTTTTTTAACTTTTTTAAGTATCTGGCGTTCAATATTGTTGAGCCAGCAAACAATATTGAAAATTTTCATATTTGGCATATTTCTTTCAATATTGGTGAGGTGCGTAACACTATTGAAAGTTACGAATATCAATGTGTGACATTTTCAATATTGGTGATTAAGGTTTTATTTCCGAATTAAAGAGCGTGATATCTGTATTTAACACCGCCGATATAAATACGTTTCCTTCATGATTTCTGGAGATGCAATGAAGATAATTACTTGCTACAAATGCGTACCTGATGAGCAGGATATTGCGATTAATAATGCTGACGGAACACTCGATTTCAGCAAAGCGGATAGCAAAATCAGCCAATATGATCTGAATGCAATTGAAGCTGCTTGCCAGTTAAAACAGCAGTTGGGAGACGCTCAGGTTGTCGCCATGAGCGTTGGCGGCAAAGCGCTGACTAATGCAAAAGGGCGCAAAGATGTCCTCTCTCGTGGCCCTGATGAACTGATTGTGGTCATTGACGATCAATTTGAGCAGGCGCTGCCGCAACACACCGCTACCGCGCTGGCCGCCGCGGCGCAAAAATCAGGTTTCGATCTACTTATCTGCGGCGACGGTTCTTCCGATCTTTATGCTCAGCAGGTTGGTTTGCTGGTGGGCGAAGCGCTGAACATTCCGGCGATTAACGGCGTGAGTAAAATCCTCTCTCTTACCGACAGCACATTGACGGTAGAACGCGAACTGGAAGATGAAGTTGAAACGCTGAGCATCCCGCTCCCGGCGGTGATCGCGGTTTCCACCGACATTAACACCCCACAAATCCCTTCGATGAAAGCCATTCTTGGCGCGGCGAAAAGACCGGTTCAGGTCTGGTCGCCTGCGGATATCGGGCTGAACAGCGT
barcode2 S. Typhi H58 + wastewater	2.2.2_2	100		GCACAGTTCATCCGAGTGATTAACAATCCACCACGCCTCTTCGTGGCGAACAAGACTGAGCGCGATATCGTCTTTCCCATGTTGCTCAAAAAGCGGAATGTAGGGGGCGGCGGCAGTAAATACGATGTATGTCCCTGCGGGATACTGTGCGTTATCCGTTATACCCTGCGACTGTATTTTCCGTAATTCCCACATGTCTTGTTTCATTATGTCCCTTAAATGTATTTATTTTTCTGGAGGAAACGTTTAGGGAGTTTTAATTCATAAATAATTTTAACTAAATTCATAGGGAGTCATTATTGATGACACCCTTTTTATTATTTTCGTCGTGAATGCATTGTTGTATGCATAGATGTCTTTTTTGAAATATTATTTCTTTTAATTCTGTAATTGCGATTTTTATCTTGTTGTTCATTGATTATTTAATATTAACGGCTTGGTTGCTAATTAGTCCCTGATCTGTATCATTGTTTTGTTTCGATATTTTGTCGAACATTTTAATAAAGAATTGTTTATATATTCATGTGCATTGATGCATTATTTTTATGAATTTTTATGTCACAAGGCATAACAAATGGAAACTCCTGTTTCACGCAGTGCGTTATATGGAAAACTGGCCGGCCCACTATTCCGGTCGCTGGAATCGGCAACGGCATTTTGCAAACTACGCTCTAATCCCTGGGGTGAGCTGACTCACTGGCTGCACCAGTTAACACAGCAGCCCGATAACGATATTCTCCACGTTCTTCGGCATTACCAGATCCCTCTTTCTGATGTGGAGAAAGCGTTACTCCGGCAACTGGATATGCTGCCCGCCGGGGCCAGCGCCATTAGTGATTTTTCTCACCATATCGATCTCAGCGTTGAAAAGGCCTGGATGCTGGCGAGCGTCCGTTACGGCGATAACAAAATTCGCAGCGGCTGGTTGCTGCTGGCCTTGTTGACCACGCCAGAACTGCGTCGGGTACTGAGCAGTATCTGCGCGCCGCTGGCCACGCTTCCGGTTGATGAACTGACGGAAATACTGCCCTCGTTGATCGAAACATCGCCGGAAGCGCAGGAGCGCCCTTACGACGGCTCCGGTCTGGCATCAGCCATTCCCGGTGAAAGCAGCCAGGCGATTCCCAACGGCGTGCAGGACGGTAAATCCGCGCTGGCAAAATACTGTCAGGACATGACGGCACAGGCGCGCGACGGCAAAATCGACCCGGTGACGGGGCGTGAGCATGAAATCCGCACCATGACGGATATTCTGCTGCGCCGTCGCCAGAATAATCCCCTACTGACTGGTGAGGCGGGCGTCGGAAAGACGGCGGTCGTCGAAGGTTTTGCCCTCGCGATTGCGCAGGGGGAAGTGCCGCCCGCGCTGCGGGAAGTACGGCTGCTGGCGCTGGACGTTGGCGCTCTGTTGGCCGGAGCCAGCATGAAAGGCGAGTTTGAATCGCGTCTGAAAGGGTTACTGGAAGAGGCCGGGCGCTCGCCGCAGCCGGTTATTCTGTTTGTCGATGAAGTTCACACTCTGGTGGGCGCGGGCGGCGCATCCGGCACGGGCGATGCCGCTAACCTGCTGAAACCGGCGCTGGCGTGCGGCACCCTGCGGACTATCGGCGCCACCACCTGGAGCGAATACAAGCGCCATATTGAGAAAGATCCGGCGCTGACCCGTCGTTTTCAGGTGTTGCAGATTGCCGAGCCGGAAGAGATCCCCGCAATGGAAATGGTGCGTGGTCTGGTGGATACGCTGGAAAAACACCATAACGTACTGATTCTGGATGAGGCGGTACGTGCGGCGGTACAGCTTTCTCACCGCTACATTCCCGCCCGGCAGTTGCCGGATAAGGCCATCAGCCTACTGGATACCGCCGCGGTCCGCGTGGCGCTGACGCTGCACACGCCGCCTGCCAGCGTACAGTTCCTGCGTCAGCAGCTAAAAGCGGCGGAAATGGAACGGTCGCTGTTGCAGAAGCAGGAAAAAATGGGGATTCAGTCAGATGAGCGGTGCGATGCGCTGACGGCGCGAATTTTCTCGCTCAACGATGAACTGACTGCATCCGAATCCCGCTGGCAGCGGGAGCTGGAACTGGTACATACGTTGCAGGAACTGCGTGTCGCAGAGTCTGATGC
barcode2 S. Typhi H58 + wastewater	2.3.1_v12	141		TTCAATAACGAAGCGATCTCCTGCAGTATTTCAGAACGTCCAACTATGCCGATGATCGATGACATGCTCATGAAGGCATTTGCCAGACTTGATGCGGGTACCAATCCGGTTCTTCATTCAGATCAGGGCTGGCAATACCGTCATTGATGGTACCAGTATCAGTTACGAGAGTTTGGCATCATCCAAAGTATGTCCCGCAAAGGCAACTGCCTTGATAATGCCTGTGCAGAATTTTTTTTCGGCACTTTAAAATCAGAAAGTTTTTACACCAGTAAATTTAAGGATATTGATGAACTTAAGATAGCTATTGAGGATTACATACGATACTACAATACCCGACGAATTAGCCTTAGATTTAACGGACTCAGCCCGGTTGAATACCGCCTAAAGAGCTATCCAGGCAGAAATTAACAAGGTCTGTACAGGGATGCTATCAGGAAACCTGAACGTTGGTGGATACGCTCACGTAAATGTCTGCTATGAGCGAGGAGCGGACGCCCTATTTCACAAAAATTAGTATTGTTCTACAAGTAACTCTCACAATGAGGTTTTATGAAAATCAGAAGGTTCAGTAATGGGGATGAAATATCGTTATTCAGAGTTTTTTTCTCATCTGTACATACGATCGCATCACACTACTACACACGTGAACAAATTGATGCTTGGGCCCCAGCAGATATCGACCTGGAGCGATGGGCCAATCACATTAAGGAATTACAACCTTTTGTTGTAGAGCTGGATGGTGAAATAGCTGGATATGCAGATGTTCAACCAAATGGATACATTGATCATTTCTTTGTATCAGGAACCTATTCA
barcode2 S. Typhi H58 + wastewater	2.3.2	452		ACGATAAACCGCTTCCGTCACCATCCCCGCCGGGTTAGTAAAGTTAATGACCCACGCATTCGGACATAATTCTTCAACATCCTTAATGATGTCAAAAATAACCGGAATGGTACGCAACCCTTTAAATAAACCGCCAGCGCCGTTGGTTTCTTGCCCCAGATAGCCGTGGCTAAGCGGGATACGCTCGTCCAGCTCACGGGCTTTGAGTTGACCAACGCGTAGCTGGGTAGTGACAAAATTAGCGCCTTTCAGCGCTTCCCGGCGATCCAGCGTTTTATACAATTTTAGCGGAACGCCTGCTTTATCAATCATTCGCTGGCAGAGATCATAAATAATGCCCAGCTTCTTTTTCCCGTCTTCAACGTCAACCAGCCATAATTCGGTGACAGGTAATTCATGGTAGCGCTTAATAAAGCCTTCAAGTAATTCAGGGGTGTAGCTGCTCCCGCCACCAATAGTGACGACTTTTAATTTCTGGCTCATAATATCTCCCTTCAGTGTATGACACTGATATGTATTACGCTATGCCCGCTCGTAAGAAATAGCGTGACGTTCCCCGCGCTATTGGGGCAAGCGTGAAATGTAACTAATCGAGCAATGTAAACCGTTACTCATTAATTTCCGTCAATCGCTTCCGATAACTATTCGGCGTGAATGAGGTCATCTTCTTAAACGTTTTAATAAACAGACTTGGACTACTGTACCCGGC
barcode2 S. Typhi H58 + wastewater	2.5_4.3.1.2.1_3.3	214		GGTTCGTTGTCCATTTCGGTATGACCAGGACGAGAAAATTTTATGACTGCGTAAAGATAATCTAAGTAAATATTTAGCATCAATGGAACATGCATGGTGCTGATTATTAAAACCACAGTGTTCAGGTAAATAAATATGGCTACCGGTCTCTAAATCAACGTCCCGAAAAAAATGAATCAAATAATCGGATAAGTCAAATCTGATGTTATTTTTCATGGGACGCCCTCTTTCAAACAGTCTCTTTTTTGCATTCCTTTAAAACCAGCACCATCATTTTATATAAAAATCATCACGAAGTATGCTTCTTTTAACGATGACATCAAATCCTCCCTCCTTTTGCATCAACTTACGTATCCCTGAAATGGCGAGACCAGGCTAAATCCACTTGAGGTTGCTCACTGAAAACCTCATCCCGGAACAAACTCAACCGCGCTTCCCCGCCACGGCCCTTTCGCCGAAAAACCGATAATGGGTATAAATATACCGCTATAAGCTATACCCACACACTTCACATTGTTTCTTATCGTTAATCCGATACGCTTTTTTCACATTATTTCTGGCGGTATACGTCGGTGCAAAGTGAATCGGGCTCGTTTCCGCGCTCGCGCGTAACACAATGATTTACCTTGCTGGCGGAACGTCAACGGACCCGCAAAAGCGCCTTATGCCCCTGGCGGAGCGTGGTGCAAAAAGGAGAAAAAATACGCGTTATGAATAACGAGGAGACCTTTTATCAAGCCATGCGTCGTAAGGGAGTGACCCGACGCAGCTTTCTCAAATTCTGTAGCCTTGCCGCCACATCGCTGGGACTGGGCGCCGGAATGACGCCAAAGATCGCCTGGGCGCTGGAGAATAAACCGCGGATTCCGGTGGTCTGGATTCATGGACTGGAATGCACCTGCTGTACCGAATCCTTTATCCGTTCCTCGCACCCGCTAGCCAAAGATGTGATCCTCTCGCTGATTTCCCTCGATTATGACGACACCCTGATGGCCGCCGCCGGCGCACAGGCCGAAGAAGTCTTTGACGATATTACCACTCGCTACGCCGGGAAATACATTCTGGCGGTGGAAGGCAATCCGCCGTTAGGAGAGCAAGGAATGTTCTGTATCAGCGGCGGCCGCCCGTTTATTGAAAAACTGAAGAAAGCCGC
barcode2 S. Typhi H58 + wastewater	3.1.1_v5	43		ATGGCTTCTGGTTGGCTTTGACCAACTGGCAATGCAGGCTTTTCAGGCCGCGCATTATGGTTTTATCTCCCGGCAAGAGCTTCACCGTAGCCTTCGACGGGGAGGCCATCTAATCCGTCAGATCTATGGTGCCGCTCAGAAATATCGTTTTTTTCAGGTGAACCGCCGCGATTTTGCATTACAGAATGCTCAGTACCATGAGGCAATCAGGAACGCAGGTGAAATTGACGAAGCTGTTTTGTTGGGGCAAAAACGTTCCTCTTTTTCACCCCCAGTCAGTAAGGAGAGTATTGAACTTCTACTGGCGGCAAATGCAAAAGCAGACAAAGCAGATATTGTGCAATTACTGTAAGAACCGTTAGAAGAACAGATTGTGGCTGACCCTTCTTTATTTGTCGCTGATTCGAAACGCATCGATGGTTAAGCCCGCAGAAAGGCTGGTTTTCTGAAAGGAGTGTTATCATGCGTCTGGTGTTGTGTGAAAAACCTTCTCAGGGCAGAGATATTGCGAAGTTTCTTGGCGCCACTCAAAGAGGCGAAGGATTCCTGAATGGTCCGGGAGTTACAGTCACCTGGGCTCGCGGCCATCTGCTGGAGACAGCTGAACCGGAAGTATATGGCGAACAGTATGGTAAGCCATGGCGCACCGATGTGCTTCCTTTATTACCACAGCAGTGGAAACTGGTAGTCAAAGCGGATGCAAAAGCCCAATTCGCGGTAATTAACCGTCTGCTTAAACAGGTAGATGAGGTGGTAATTGCCACGGATGCTGACCGGGAAGGTGAAGTAATCGCCCGTGAGTTGCTGGATTACTGCAAGTTTCAGGGGCGTGTATTCCGGTTGTGGATGTCAGCTCTGGATGATGCCAGTATCCGGTCAGCGTTAGCTGATTTGTGGCCGTCTTCCCGAACTGAATCGCTTTATTATGCTGGCGTGGGCAGGAGCAGGGCTGACTGGCTGATCGGTATGAATCTGACTCGCCTGTTTACACTCCTGGGGCGTGAAGCGGGTATCGGTAACGTACTTTCAGTTGGCCGGGTACAAACGCCAACGCTGGCGATAGTGGTAAAGCGTGATCGTGAAATTGATAACTTCGTGTCGAAACCGTACTTCGAAGTTATTGCCACGATGGCCGTGAATGGCGTGTTGTT
barcode2 S. Typhi H58 + wastewater	3.3.1	112		TCCGTTTTGCGAAATCGTTCCCGGAAAAATGATCCATTTCTGTCACACTCAGAACGATTTGATAACAACAAGAGGTCATAGGGATGAAAAAATCATTACTCGCTGTTGCTGTGGCAGGGGCTGTTTTGTTGTCATCCGCCGTACAGGCGCAGACAACGCCGGAAGGTTATCAATTACAACAGGTGCTGATGATGAGCCGCCATAATCTGCGGGCGCCGCTGGCGAATAATGGCAACGTACTGGCGCAGTCGACGCCGAACGCCTGGCCGGCGTGGGACGTTCCCGGCGGGCAACTGACGACGAAAGGCGGCGTGCTGGAAGTCTATATGGGACACTACACACGTGAATGGCTGGTCGCGCAGGGGCTGATACCGTCGGGAGAATGTCCGGCGCCCGACACGGTATATGCCTATGCGAATAGTTTGCAGCGCACCGTCGCCACCGCGCAATTTTTCATTACCAGCGCTTTCCCCGGCTGTGATATTCCTGTTCATCATCAGGAAAAAATGGGCACTATGGACCCTACCTTCAATCCGGTGATTACCGATGATTCCGCCGCGTTCCGGCAACAGGCCGTACAGGCGATGGAAAAGGCGCGTAGTCAGCTACATCTTGATGAGAGTTATAAACTGCTTGAGCAGATAACGCATTATCAGGACTCGCCGTCCTGCAAAGAGAAGCATCAGTGTTCGCTAATCGACGCGAAAGATACCTTCAGCGCGAACTATCAGCAAGAGCCTGGCGTGCAGGGGCCGCTGAAAGTAGGGAACTCGCTGGTGGATGCGTTTACCCTGCAATATTACGAAGGCTTTCCGATGGATCAGGTCGCTTGGGGCGGGATCCACACCGATCGGCAGTGGAAGGTGCTGTCAAAACTGAAAAACGGCTACCAGGACAGCCTGTTTACCTCACCCACGGTGGCGCGCAATGTCGCTGCGCCGCTGGTAAAATATATCGATAAGGTGCTGGTTGCCGAGCGCGTTAGCGCGCCGAAGGTTACCGTGCTGGTGGGGCATGATTCCAATATCGCGTCGCTGCTGACGGCGCTGGATTTTAAACCCTATCAGCTCCATGACCAGTATGAGAGAACGCCGATTGGTGGTCAGCTTGTCTTCCAACGCTGGCATGACGGTAACGCTAACCGGGATTTGATGAAAATCGAGTATGTCTACCAGAGCGCC
barcode2 S. Typhi H58 + wastewater	4.3.1.1	162	Pos:456 (94%) , Change:T>C, Implication: 4.3.1.1	CTGGCCTGATACCTGGATGTATACCGCCAACACCAGCGATGTCGCTATTCTCAAGCGAGCGCACCAAAAGATGGTGAAAGCTGTCGATACTGTCTGGAAAGGTCGGGCCGAGGGGCTGCCTTATAAAGATCAGAACCAACTGGTGACAATGGCCTCGATTATTGAAAAAGAGACGGCTGTCGCCAGCGAACGCGATCAGGTGGCCTCAGTCTTTATTAATCGCCTGAGAATCGGTATGCGCCTTCAGACCGATCCCACCGTGATTTACGGGATGGGGACGAGTTATAATGGTAACTTGTCGCGTGCGGATCTGGAAAAGCCGACGGCTTATAACACGTATACCATAACCGGGCTGCCGCCAGGACCGATTGCATCGCCCAGCGAAGCGTCATTGCAGGCGGCGGCGCATCCGGCGAAAACGCCGTATCTCTATTTTGTGGCCGACGGTAAAGGCGGCCACACATTTAACACCAATCTTGCCAGCCATAATCGGTCAGTGCAGGAGAAAGTGCTTAAGGAAAAAAATGGGCAGTAATTATATCGTCATCGAGGGCCTGGAAGGCGCCGGAAAAACCACTGCGCGCGACGTGGTGGTGGAGACCCTTGAGCAACTGGGTATTCGTAACATGATTTTTACCCGTGAGCCGGGCGGTACGCAGCTTGCCGAAAAACTAAGAAGTCTGGTGCTGGATATCCGATC
barcode2 S. Typhi H58 + wastewater	4.3.1.1.P1_v2	59		TAGGTCGACCAGCGCAAATTCATGACTGTATAAGGCTTTCGCCATATCCGGTTTCACAAACATATTATGCCAGTTAAGGCTATAGGGCCACGGGCTTTCCGGACCGTGATAAAAGAGGATTGGTACCACCAGCGGCAAGGTATCATGGCCGGCATCCAGATGACGCTGCATGGCGGCAATGGCGTACCGCATCAGGCGAAAAGCCATCAGCCGGTCTGATTTGCTCTGATGTTCAATAAGCGCGTAAACATACCCGGGGCCGTGTTGGGTATGCAGAGAGTAGAGAATATCTGAATAGCGGCTGCGTAAATTGTCTTCAACAAAACTCCCCGACTCCAGCTTCAGTGAATCCAGATCGCAGATTGCAAGAAAGTCTTCTGGCAAGTGGATAGCCAGAAAGTCGCGGGCGACCTCTTTTTGCATCAGCATCTGTCGGAATACCGCATCGTGCGGCGTGGTGGGTAGACGTTCCATGCCCCGTCCTTTGTTGCCTGACTGTAGCGACCACTTTGTCAGCGACAACGAGGACAAACCAGGGGGCTATTACTCTGTTTGCGAGTCGTCTTCCGTACTTTTTAACTTGTTTTCATAATCACGCATAACTATTTCCAGCGCGCGTAGCACCGTTCGTGCCGGTAAGCGATTCTCTTCAAGCAGCACAATTAAATCCACGGCCAGTTTGACTTCATCAGGGGCATTTTCAAGCGACATACTTTCTCCTGGGTTAACGGG
barcode2 S. Typhi H58 + wastewater	4.3.1.2.1.1_4	245	Pos:1047 (99%) , Change:G>A, Implication: 4	CAGGCCTGGTTTGACAATCTGTTTGTCCGTCAGGATCTCGGCAATCAGTATTATCTCCAGGCTGGTCGGATGGATCAGCGGAATCTGTCCAGCGCCACGGGGGGGGATTTTGGGTTCAGTCTGCTTCCCCTGAGCCGGTTTGATGGATTACGAACCGGGACCACCCAAGCTTATGTTAACCATGAGGTGGACCATAATGCCACTCCGGTTATGGTTCAGGTTACCCGAAATGCCCGTATTGATATTTATCGTGGCAGCGAGTTGCTGGGGAGTCAGTTCCTGACCCCGGGAATGCATACCCTGGATACTCATTCTCTTCCACCGGGAAGCTATCCTCTGGCGTTGCGGGTGTATGAGGATGGGATTCTGCGGCGAACGGAGACCCAGCCCTTCAGTAAGGGGGGCAATAGCTTCAGTGCACAGACCCAGTGGTTTATTCAGGGCGGGCTGGAAGATACCGGGGATAAAGCCAGCCATTATGACGGTGAGACTGTCATGGCTGCCGGATTCCAAACTGGGCTGCGGAAAAATATCAGTCTGACCGAAGGTATCTCTCTGGCACATGAGGCCTGGTACAGTGAAACCCGACTGAATTCACAGCATGCAGTGCTGGATGGCACGCTGGACCTTTCTGCCGGGATACTGCATGGGACAGACAGCACGAGCGGTAACACTGAGCAGGTGACATACAACGACGGATTTTCCGCGAGTCTGTGGCGTAACCATACGGAAAGTGATGCCTGTAGTGGTCGTCATCCACAGTCAGTGCATGCCAGTATGACCTGCCAGACTTCGATGAACGCCTCCCTGTCGGTTTCGGTGGGGAACTGGTATGCCCTACTGGGATACAGTACCAGCAGGACAGAAGGTCGGCCGGTTTACCGGGGATATGATGATAACAGTGACAAAGAAAATGTGTTCTGGCGACAGGCATACATCCCTGCCTCTCACCGCGAATCTGCTCAGGCTAGTGCAACGTACAGCCTTAATATGGCTGGCATGAATATTAATACCCATGGGGGAGTATGGCGAACCCGAAATGACGGAATGAATGATGATGGCTTGTTTATGAGTGTCAGTGTGTCATATGCCTCTCAACCACCGACAATGACTGGCAGTAATAGGTATACCTCAGCCGGGACCGATATTCACAGTAGCCGGAATCAAAAAACACAGACGTCCTGGAATGTGAACCATGTGAGATCCTGGCAGCAGGATCTGTATCGTGAACTGTCGGTGGGTTTCTCCGGTTATAACGACGACAGCTGGAGCGGGAGTCTCGGCGGACGCATGAGCGGCCGTATGGGTGAACTGAGCGCCACTATCAGTAACTCCCATCAACGTAATGCGGGCAGCGCCAGTTCACTCACCGCTGGCTACAGCTCGTCTCTGGCGTTATCCCGTAATGGACTGTTCTGGGGAGGTGGTCAGGACGGTGAACCGGCCTCTGGCATGGCGGTGAACGTGGAGTCAGAGGGGGACGAGGGCAGTAGCGGGAAAGTAGTCAGCGTTCGTGGCAGCAGCCAGCCGTTCAGTCTCGGTTTTGGTCAGCAGTCGCTGTTGCTGATGGAAGGCTATAACGCCACGGAGGTGACCATTGAGGATGCAGGGGTTAGTTCACAG
barcode2 S. Typhi H58 + wastewater	4.3.1.2_v3	8		TGTTTCTGGCTTCGCTGCTGGGGGCTGCGCTGGACTTTCGCCAGATTGCGTTTCCGGCGTCTGAGAAGGCGCTGGCGTCGCAGGCTGACTGCTGGCGGCCGGCGTCGCCTCGGTTTTAACATTATTGTCATCACATCCTGTTGCGCCCAGGGTCATTAGCGCAATGATTATCGCTGAGGATAATAAATTCCTTTTCATTTAATTGCCTTTTGTATATTTACGTTGGGGTTCTCTTATTTTAACGAACACATTGATATTGATAATGTTAATTATAATGAAATATGGATTAAGTATTTTTTGTGTTGAATAAATCACATACCTGTTTTTTTCATTAAAATGAATCTGTAAATTTCAATGATATTATTTATAGGTTATTCTAATGAAAAAGGATTTGTTATCATCAATTATTATCGCTATGCTGATGACTGCCGGGCTAAGCGCTTGTGATGAAAAAAAAGCGGACGAACAACCTGTAGCTCAGAGTGCGGATTCATCAGCGAGCAATACACAATCCACATCAGCGGAAAGCGCAGATGCGAACGATGTTCTTAACCAAAAGCTGAATGTTTACATTGATTGTTATAATAATCTCCAGGCAGATATTTACCGTGCTGTAAATCGTTATGCTAACACATTCGACGATTTCCGCACCGGTCCTACCGGTAAGGAAGACGATCCCTCTCCGCTGGTTCCTGTGTATCCTGCATTTATCCAGGACTGCCGGAAAGACATC
barcode2 S. Typhi H58 + wastewater	parC_v7	11		TGGCACAATCACTAAACGCGTCGGGTTTTCGTGATCCGATTCATCGCGCAGGTCGTCCACCATCGGCAGTTTTTTATTGCGCATCTGCGCAGCAATCTGCTCCAGCACTTTTGCGCCAGATACCTGATGCGGCAACGCGGTGATCACCACGGCGCCGTCTTCTTTGGTCCATACCGCGCGCATACGCACGGAGCCACGCCCATTTTCGTAAATTTTACGAATTTCCGCACGAGGGATAATGATCTCCGCTTCGGTCGGGTAATCCGGCCCCTGGACGATATCCAGCAACTGATCCAGCGTCGTTTTCGGCTGCTCAATCAGCGTAATCGCCGCTTTCGCGACTTCGCGCAGGTTATGCGGCGGAATATCTGTTGCCATGCCCACCGCAATACCGGTGGTGCCGTTCAGCAGGATGTTCGGCAGACGCGCCGGTAACATTTTCGGTTCCTGCATGGTGCCGTCGAAGTTTGGCACCCAGTCCGCAGTCCCCTGACCGAGTTCGCTTAACAGCAGCTCGGCGTATTTGGACAGGCGGGATTCGGTATAACGCATCGCCGCGAATGACTTCGGATCATCCGGCGCGCCCCAATTCCCCTGGCCATCGACCAGCGGGTAACGGTAAGAGAACGGCTGCGCCATCAGCACCATGGCTTCATAGCAGGCGCTGTCGCCATGCGGGTGATACTTACCCAGTACGTCG
barcode2 S. Typhi H58 + wastewater	tviD_v2	298	Pos:430 (95%) , Change:C>T, Implication: known, but uninformative allele	GCAAGCTGCTTAGTGATCGATAAGGTAATCTCACGTATTTGGTCCTGTTTCTCTTGTCGCCCCTCATCAAGATGATGATTAGTATTATTGATCACTCCCTTAAAAATAGCCGCAACGATCGCGTCACCAAACATATCGGTATAATGAGTAAGATCGTCGCCATTTTTTTCCAGGGCTCGTTTCTGCCCCCACTTTTCCATCAAATTTGTCGGGTTAACGCAGGGAATATCCATCCTGGCGGCGATGGTGTCGACATTTTTAATCAACCGACTACGGGATAGAATGACGGTTCCAGCACGAGTCACGGCATCAACATGTGTCATAAACATAACGCGATCGCGACCAAGAAGCTGAACGATTTCCATCATATCCTGTTCGATAGCATGCTCATCCATCTGCTCGACATTGATATTGCTTAATAAGGCACGATTGTCTTCCGACATTCCGGCAAAACAGGGATCGTCTTTGAGATAGGCCAGCAGTTTGTGTCGATTTCCTTGCGTGGCCAACGACCAGTACATGCACGCCCGCTCTGTTTGGCTAAAAAATTCATAGAAATGACGAGTTAAATAATTTATTTGTAAGCAGAACCCATAGGCCATAATCTTCTTCTGACTTGAAATCTCAATGATATAGAAATCAGAACGACTATGTACGTCGGTGTTTGAATAGTTTACATTAGGTCTAAAAATAAATGGTCGGACCTTTTCAGGAATGTCTATCAAGCCCAAAATAAACCGAATCTGCTGTAATGCCTCGCTGCTCGTATGCGTAAAACCATATATTCTCTTAAAGTTTGCCTGAAAATTAAAATAAGGC
barcode2 S. Typhi H58 + wastewater	acrB_v2	510		CACAGGAAGACGACGATTAGCGAGATAGCATACAGGGCAGGGGCCTGGTTGCCGGACAACCGCTCCTGGTAGGACATCCCGGTCCAGTCATACCCAATGCCTGACGGCAGCTTGCTGGCCAGTTCTTCCATCATCGCCATCGCTTCACCAGTACTCTTGCCTGGCGCCGCCTGACCCAGAATTTCCATCGAAGGCAGACCGTTATAGCGTTCCAGACGCGGCGAACCATATTCCCAGCGGGAAGAGGAGAATGCGGAGAACGGCACCATCTGACCATCGCTACCACGAACGTACCAGTCGTTAATATCATCCGGCAACATGCGGTATTTCGCTTCGGACATCACGTAAACTTTCTTCACACGACCGCGATCGATAAAGTCGTTTACATAGCTGCCGCCCCATGCTGCGCCCAGCGTGGTATTAATGTCGCTAATAGACACGCCCAGCGCCTGAGCTTTTTCCTGGTCGATATCGATTTTAAACTGCGGCGTATCTTCCAGACCGTTAGGTCGAACGCCGACCAACAGATCAGGATATTTCGCCACCTCGCCGAACAACTGATTACGTGCCTGGGTGAGTTTTTCGTGACCAAGTCCCGCCTGGTCAATCAACTCGAAGTCAAACCCGGTTGCGGTGCCCAGTTCAACAATCGCCGGTAGGTTAAAGGCGAAGACCATCGCATCTTTAATTTGTGAAAACGCTGCGGTTGCCCGCTGGGTAATCGCTTCAACCTTGTTTTTTTCGCCTGGACGATCGGCCCAGTCTTTCAACGACACAAATGCAATACCGGTATTCTGACCGCGCCCTGCAAAACCGAAGCCGTTGACGGCGAATACCGATTCAACGTTGGCTTTCTCTTTGTTCAGATAGTAATCCGTGACCTCATCCAGCACTT
barcode2 S. Typhi H58 + wastewater	gyrA	93	Pos:320 (97%) , Change:C>T, Implication: Unknown Pos:1684 (99%) , Change:G>T, Implication: gyrA_S83T	GACGCCTTCTTCGTACTCACGAACCGGCAGAATCGCGGTGATACGTTCGTTGGCTTCCAGCGGCAGCAGGTTAACGATCGGACGACCGCGCGCGCCACGGCTGGCTTCCGGCAACTGATAGACCTTCATCCAGTACAGACGGCCCCGGCTGGAGAAGCAAAGGATGGTGTCATGGGTGTTGGCCACCAGCAGGCGGTCGATAAAGTCTTCTTCTTTAATACGTGCTGCTGATTTGCCTTTACCGCCACGACGCTGTGCTTCGTAATCGGTTAACGGCTGATATTTCACATAGCCCTGATGAGACAAGGTTACGACAACATTTTCCTGGCTAATCAGATCTTCGATATTAATATCGGCGCTGTTGGCGGTGATTTCGGTACGACGCTCATCGCCGAACTGATCGCGAATTAACTCCATCTCTTCGCGGATCACTTCCATCAGGCGATCGGCGCTGCCCAGAATGTGCAGCAGTTCAGCGATCTGCTCCAGCAACTCTTTGTATTCGTCGAGCAGTTTTTCATGCTCCAGGCCGGTCAGTTTCTGCAAACGCAGATCCAGAATCGCCTGCGCCTGCTGTTCAGTCAGGTAGTATTGACCGTCACGCACGCCAAATTCTGGCTCCAGCCATTCCGGACGCGCGGCGTCGTCACCGGCGCGCTCCAGCATCGCAGCAACGTTGCCCAGATCCCACGGACGCGAAATCAGCGCCGCTTTCGCTTCCGCCGGCGTCGGCGCGCGGCGAATCAGTTCGATAATCGGGTCGATGTTGGCCAGCGCAATCGCCAGAGCTTCAAGGATATGCGCACGATCACGGGCTTTACGCAGTTCAAAAATAGTCCGACGCGTCACCACTTCACGGCGGTGGCGCACGAACGCTGAAATAATATCTTTCAGGTTCATGATCTTCGGCTGGCCGTGATGCAGCGCCACCATGTTAATACCGAAGGAAACCTGTAGCTGGGTCTGGGAGTAGAGATTATTAAGCACCACCTCGCCCACCGCATCGCGTTTCACTTCAATCACGATGCGCATCCCGTCTTTGTCGGATTCGTCACGCAGCGCGCTGATGCCTTCCACGCGTTTATCTTTCACCAGCTCGGCGATTTTCTCGATCAGGCGCGCTTTGTTCACCTGATAGGGAATTTCATGGACGATGATGGTTTCACGGCCCGTTTTCGCGTCAGCTTCAACTTCCGCGCGGGCGCGAATGTACACTTTGCCACGACCGGTACGGTAGGCTTCTTCGATACCACGACGACCGTTGATGATCGCGGCGGTCGGGAAGTCCGGACCCGGAATATGTTCCATCAGCCCTTCAATGCTGATGTCTTCGTTGTCGATATACGCCAGGCAGCCGTTAATCACTTCCGTCAGGTTGTGCGGCGGGATATTCGTCGCCATACCTACTGCGATACCGGAAGAACCGTTCACCAGCAGATTCGGAATTTTGGTCGGCATGACGTCCGGAATTTTTTCCGTACCGTCATAGTTATCCACGAAATCCACCGTCTCTTTTTCGAGATCGGCCATCAGTCCGTGGGCGATTTTCGCCAGACGGATCTCCGTATAACGCATTGCCGCCGCGGAGTCGCCGTCAATAGAACCGAAGTTACCCTGACCATCCACCAGCATGTAACGCAGCGAGAATGGCTGCGCCATACGAACGATGGTGTCATACACTGCGTAATCGCCGTGGGGATGGTATTTACCGATTACGTCACCAACGACACGGGCAGATTTTTTATAGGCTTTGTTCCAGTCATTGCCCAATACGTTCATGGCGTAAAGTACGCGACGGTGTACCGGCTTCAGGCCATCTCGGACATCCGGCAGCGCACGGCCAACAATGACAGACATCGCATAATCCAGATAGGAGCTCTTCAGCTCTTCCTCAATGTTGACCGGTGTAATTTCTCTCGCAAGGTCGCTCATCTAACCGCTATCCCTCTACTGTATCCCGGATTCAAAGGTCGCAAATTATAACACATTCGCCCACGTACTGGTAAACGGAATGCAGCCAGACAATGCTTTATTCGGGTGCCACATGCTCTCTTCATTTATAAGCGTGGTCTCGGCGTTTATCGGCGATCAGCTTCA
barcode2 S. Typhi H58 + wastewater	plasmid_ST6_C19241A	0
barcode2 S. Typhi H58 + wastewater	chromosomal_MDR_cyaA	0
barcode2 S. Typhi H58 + wastewater	chromosomal_MDR_yidA	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_AL513383.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_CP029645.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_CP029879.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_CP029924.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_CP029957.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_LT904879.1	0
barcode2 S. Typhi H58 + wastewater	plasmid_MDR_LT904892.1	0

Model Signatures

Back to Summary

Amplicon	Is Core	Signature	Date Trained
1_3_4.3.1	True	c6a124cc-2d1a-439d-b218-82f0169d7dce	17/Jun/24 at 14:11
2.2.2_2	True	d42fe4cc-a399-4939-afc7-a91b1a1d78ba	17/Jun/24 at 14:14
2.3.1_v12	True	05c89613-314d-4021-9f7f-450db4e3d6bf	17/Jun/24 at 14:10
2.3.2	True	3760123e-71b1-45d4-a81e-f514999694f2	17/Jun/24 at 14:15
2.5_4.3.1.2.1_3.3	True	39f7a587-e9d6-4e67-8d3e-5bac1ac29d81	17/Jun/24 at 14:16
3.1.1_v5	True	ff776cf6-a3bb-4622-bf05-e48620629afe	17/Jun/24 at 14:16
3.3.1	True	696621aa-ab6c-4056-8825-0740f6006db1	17/Jun/24 at 14:16
4.3.1.1	True	52575983-1e91-4f23-b792-095e94a5d30d	17/Jun/24 at 14:17
4.3.1.1.P1_v2	True	599113c8-2f29-4cfc-98cd-95b14bdc656c	17/Jun/24 at 14:17
4.3.1.2.1.1_4	True	983bccd2-b31a-45c8-ae85-6380b891601b	17/Jun/24 at 14:18
4.3.1.2_v3	True	52e276eb-b247-45e6-8d99-12328a8c031d	17/Jun/24 at 14:18
acrB_v2	True	ce95b108-2039-48a5-8026-49de40cd4734	17/Jun/24 at 14:19
chromosomal_MDR_cyaA	False	d48a9018-4a6d-4666-90a8-0afcf5d8c10c	17/Jun/24 at 15:08
chromosomal_MDR_yidA	False	20dbc1d7-4a1f-47db-a94a-f0199c93ca2c	17/Jun/24 at 15:23
gyrA	True	63c9a7d3-1ed2-48eb-9e75-1e61f850e827	17/Jun/24 at 14:20
parC_v7	True	0e26df39-abe8-45e7-86b1-215c43eb232c	17/Jun/24 at 15:05
plasmid_MDR_AL513383.1	False	b58fd6b7-b7d0-483c-af7a-2560d0cd76f5	17/Jun/24 at 15:58
plasmid_MDR_CP029645.1	False	cbfed9cf-b65b-4d52-96d7-df4bc4d8755a	17/Jun/24 at 16:05
plasmid_MDR_CP029879.1	False	78c9f944-6bad-4609-bc5e-2246e99a9e35	17/Jun/24 at 16:26
plasmid_MDR_CP029924.1	False	de9bd183-f458-4df1-bb51-c910db5130d0	17/Jun/24 at 17:29
plasmid_MDR_CP029957.1	False	2f098d3f-8505-48cd-b12d-0731a746d15e	17/Jun/24 at 17:38
plasmid_MDR_LT904879.1	False	126fbedc-967d-404d-b131-0e1cced3a679	17/Jun/24 at 16:09
plasmid_MDR_LT904892.1	False	c14ee0aa-de18-4fc7-8196-641b6613ae06	17/Jun/24 at 15:31
plasmid_ST6_C19241A	True	1bddb687-fd77-40a7-8183-4a3a39d735be	18/Dec/24 at 12:26
tviD_v2	True	3149a8ad-4c47-41de-91ed-1002f41f759c	17/Dec/24 at 18:13