Table 1 Summary of sequencing metrics per run and amplicon, including the average number of reads, mean depth, mean base quality, mapping quality and coverage.

Run	Amplicon	Nr. reads	Coverage	Mean depth	Mean base quality	Mean map quality
1 (n = 3)	1	1,140.33	100.00	1,032.78	24.73	60.00
1 (n = 3)	2	2,518.00	100.00	2,114.96	21.70	59.97
2 (n = 11)	1	94,641.82	100.00	52,778.65	24.28	59.99
2 (n = 11)	2	51,155.73	97.83	43,459.04	21.48	60.00
3 (n = 96)	1	1,280.92	100.00	957.67	19.42	59.98
3 (n = 96)	2	686.47	99.99	498.90	18.81	59.97
4 (n = 8)	1	6,021.5	100.00	5,300.46	19.13	59.98
4 (n = 8)	2	4,704.38	100.00	27,452.97	18.50	59.99

Mean base quality reflects the confidence of each base call, while mean mapping quality reflects the confidence that reads are correctly aligned to the reference. Coverage represents the proportion of the genome sequenced, and depth indicates the average number of times each base is read. ‘n’ represents the number of samples processed at each run. data shown were collected at flow cell exhaustion. Detailed metrics for each sample and run are available in supplementary data 3.

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