TABLE 1.

Contingency table comparing SNP calling between Medaka and Nanopolish for all three time points. Displayed are total counts across all sites called as either reference (Ref), SNP or unknown (N). Only genomes present in each category (Full Run, Run Completed and Sample Completed) are included in the analysis.

	Medaka
		Full Run			Run completed			Sample completed
		N	SNP	Ref	N	SNP	Ref	N	SNP	Ref
Nanopolish	N	151,292	29	418	183,709	32	412	837,973	116	253
	SNP	25	10,727	5	26	10,697	6	78	9,984	13
	Ref	24	0	9,818,580	33	0	9,786,167	37	2	9,132,765