. 2024 Apr 23;12(6):e04139-23. doi: 10.1128/spectrum.04139-23

TABLE 1.

Assay information and sequence

Type of target	Locus	Primer	Primer (5′−3′)	Melting temp	Amplicon length	Amplicon length + UT	Position in Amplicon	Reference	Variant	Sequence ID	Start	Stop	E. coli hits (n = 31630)	NN hits (n = 528)
E. coli species	B21_02246	Forward	GAGCGTATCTCTGAACAAGG	59.7	110	146	N/A	N/A	N/A	https://www.ncbi.nlm.nih.gov/nuccore/CP032667.1/ CP032667.1	1389110	1389219	31485	0
E. coli species	B21_02246	Reverse	GAAGCTTCRYTGGTCAGTTC	60.8	110	146	N/A	N/A	N/A	https://www.ncbi.nlm.nih.gov/nuccore/CP032667.1/ CP032667.1	1389110	1389219	31485	0
MSS - SNP	B21_00966	Forward	CAGCATAAAAGAGGAGGATG	57.9	150	186	49	A	G	CP032667.1	2863461	2863312	31582	46
MSS - SNP	B21_00966	Reverse	CTGGTTCCKGATACCGATAG	59.9	150	186	49	A	G	CP032667.1	2863461	2863312	31582	46
MSS - SNP	B21_01903	Forward	CATTCGACTCCGGTTKATTA	58.5	147	183	37	T	C	CP032667.1	1797701	1797555	24981	163
MSS - SNP	B21_01903	Reverse	GAAGAAAGCTCAATGGTTCT	58.2	147	183	37	T	C	CP032667.1	1797701	1797555	24981	163
MSS - SNP	B21_01907	Forward	CGYGAATCAAAATACATCAT	55.8	176	212	114	G	A	CP032667.1	1792511	1792336	31593	528
MSS - SNP	B21_01907	Reverse	TTCAGTTTTTCCATNGTTTC	55.9	176	212	114	G	A	CP032667.1	1792511	1792336	31593	528
MSS - SNP	B21_01912	Forward	TAGATTTAATYRACGGSACB	57.3	181	217	120	C	T	CP032667.1	1788231	1788051	31047	505
MSS - SNP	B21_01912	Reverse	TTAATCARYRGGATTTGA	52.4	181	217	120	C	T	CP032667.1	1788231	1788051	31047	505
MSS - SNP	B21_01973	Forward	AGATCCAGACYAAYGAYGAR	59.6	214	250	113	A	G,T	CP032667.1	1724304	1724091	31584	525
MSS - SNP	B21_01973	Reverse	CTGTCWACCGTCTGRATWAT	58	214	250	113	A	G,T	CP032667.1	1724304	1724091	31584	525
MSS - SNP	B21_03426	Forward	CATCACATCGCAGTATTCAT	58.1	235	271	121	G	A	CP032667.1	91517	91283	31602	527
MSS - SNP	B21_03426	Reverse	CAACAACGATATGCAKGAG	57.4	235	271	121	G	A	CP032667.1	91517	91283	31602	527
MSS - SNP	B21_03444	Forward	AAGATGRGYCAGMACRTTRT	60.7	193	229	88	G	A	CP032667.1	72607	72415	31630	434
MSS - SNP	B21_03444	Reverse	GGGCTGGATTATCATTCATT	58	193	229	88	G	A	CP032667.1	72607	72415	31630	434
MSS - SNP	B21_03573	Forward	GCTTTGYTGCAGACCATC	60	182	218	124	C	T	CP032667.1	4594237	4594056	31604	374
MSS - SNP	B21_03573	Reverse	TGATTGTGAAATACDGTGAA	56.3	182	218	124	C	T	CP032667.1	4594237	4594056	31604	374
MSS - SNP	B21_04060	Forward	ATCTAYAAAGCGATGATKGA	56.9	172	208	66	T	G,C,A	CP032667.1	4072460	4072289	31605	527
MSS - SNP	B21_04060	Reverse	AYTCTTCTTTTGCGGTATCA	58.7	172	208	66	T	G,C,A	CP032667.1	4072460	4072289	31605	527
MSS - SNP	B21_04066	Forward	AGTTTATGGAACARYACCAC	58	144	180	75	G	A	CP032667.1	4065665	4065522	31615	527
MSS - SNP	B21_04066	Reverse	CCAGCGTATTAARATGGAAG	57.4	144	180	75	G	A	CP032667.1	4065665	4065522	31615	527
SLIM v1	B21_02129	Forward	TGTCATTAGTGAAGCCTCTA	58.1	262	298	N/A	N/A	N/A	CP032667.1	1525852	1526113	31575	517
SLIM v1	B21_02129	Reverse	TTGCTGTTTTATCATGGC	56	262	298	N/A	N/A	N/A	CP032667.1	1525852	1526113	31575	517
SLIM v2	B21_01711	Forward	MTTGTGGCAATWTCTTGAYG	58.3	279	315	N/A	N/A	N/A	CP032667.1	2045846	2045568	31562	165
SLIM v2	B21_01711	Reverse	AARTTGGCRACHACCTTCG	61.4	279	315	N/A	N/A	N/A	CP032667.1	2045846	2045568	31562	165