Table 2:

Sequencing, mapping, and assembly statistics for a 4 h MinION run

Sample	Cq	Total reads	Mean length	Total filteredreads	Meanlength (filtered)	%Reads mapped (filtered)	Median depth (filtered)	Minimum depth (filtered)	Total N’s (UTR masked)	Total SNPs
AKL-MU-1	20.3	114 879	509	89 107	592	97.8	1389	462	9	8
AKL-MU-2	20.6	58 899	457	39 195	579	92.7	575	167	4	7
AKL-MU-3	25.7	56 842	459	40 216	560	95.4	568	130	9	9
AKL-MU-4	28.5	53 001	488	39 094	582	93.8	510	116	8	10
AKL-MU-5	31.2	45 168	489	33 326	587	96.5	531	85	4	7

The filtering steps remove reads shorter than 250 bp and longer than 1500 bp. C_q indicates the value for the N1 gene. The values for the N2 gene are similar. SNP, single nucleotide polymorphism.