Table 2:

Final discrepant SNPs between the Illumina data and ONT data for Case A

SNP	Position	Base in reference	Base in Illumina	Depth in Illumina	Base in ONT	Depth in ONT	Variant	Locus tag	Annotation
1	270,595	C	A	46	C	141	A	ECs0237	rhsC
2	379,516	A	G	114	A	100	G	NON CODING	N
3	1,681,338	C	G	59	C	61	G	ECs1685	Alanine racemase 2
4	1,681,339	G	C	57	G	61	C	ECs1685	Alanine racemase 2
5	2,636,513	T	C	91	T	69	C	ECs2674	Hypothetical protein
6	4,709,195	A	A	86	G	82	G	ECs4673	Membrane-bound ATP synthase epsilon-subunit AtpC

Also shown is the base as it is in the reference, the Ilumina called base and read depth at that position, and the same for the ONT data. Finally, also included is the locus tag relative to the reference genome and the gene annotation.