Table 2. MinION sequence summary.

Sample ID	Template of LAMP	Number of reads*	Total reads bp	Average reads length	Number of sequence aligned†,	Average of major allele %‡	Minimal Coverage§
11555/2016	RNA	17,451	12,729,036	729	12,335	94.8	4,229
01294/2016	RNA	8,317	5,100,998	876	5,055	94.4	1,845
03196/2016	RNA	2,988	7,177,214	863	6,952	94.5	2,495
9327/2016	RNA	5,825	2,886,343	966	2,285	94.5	837
9327/2016	serum	2,336	2,432,949	1,042	1,567	94.2	505
1268/2016	serum	5,101	3,824,032	750	3,463	94.5	1,143
7209/2018	RNA	23,285	18,516,153	795	18,607	94.2	7,596
7214/2018	RNA	20,250	16,213,247	801	15,893	94.2	6,615
7242/2018	serum	16,463	12,769,769	776	13,689	94.3	5,327
7358/2018	RNA	9,386	7,676,569	818	8,407	94.2	3,490
8232/2018	serum	30,311	24,252,642	800	25,221	94.2	9,842
2285/2018	serum	22,375	17,944,288	802	19,093	94.3	7,739
2745/2018	RNA	14,920	12,180,109	816	12,993	94.3	5,305
2926/2018	RNA	9,874	8,086,328	819	8,288	94.3	3,480
3028/2018	serum	21,576	17,383,960	806	17,752	94.3	6,674
3200/2018	serum	31,780	25,038,530	788	25,425	94.2	1,0144
S27	RNA	5,648	2,194,824	389	4,096	94.0	1,610
SL10571	RNA	1,035	392,715	379	1,029	93.5	416

LAMP products amplified from patient RNA or serum were processed for MinION sequencer.

*Number of reads: number of the quality "passed" sequences.

^†Number of sequence aligned: The obtained reads were blasted against reference genome SL11131 (156 bp: 10,317–10,472), and all the hit were clipped and mapped against reference again by bowtie. The number of mapped reads were shown.

^‡Average of major allele %: The average percentage of the called dominant allele for each reference nucleotide position (F2/B2 region removed 117 bp: 10,336–10,452). The bi-allelic loci (position 10,437) was excluded from the calculations.

^§Minimal coverage: The minimal number of reads that were aligned to reference bases (10,336–10,452).