Table 1:

Breakdown of the total number of variants of each technology against the reference genome, followed by the numbers of masked variants within prophage or methylated positions

Variants and reason for omission	Case A		Case B
Total No. of variants against the reference genome after quality filtering	2,076		1,424
Total No. of variants with masked due to location in phage	708		531
Total No. of discrepant variants called between Case A and B alone	266		101
Variants and reason for omission	Illumina VCF	ONT VCF	Illumina VCF	ONT VCF
No. of discrepant variants in each VCF	5	261	6	95
No. of discrepant variants with methylated positions masked	0	260	0	94
Final discrepant variants	5	1	6	1