Table 2.

Statistics of raw data quality.

Sample name	Total reads	Total reads (bp)	GC%	Error rate (%)	Q20 (%)	Q30 (%)
cont1	67572136	10135820400	48.61	0.11	98.64	96.29
cont2	66474707	9971206050	47.63	0.11	98.75	96.62
infect1	69033293	9854993950	49.75	0.13	98.26	95.53
infect2	70292999	10543949850	49.98	0.13	98.33	95.57

Total reads: statistics of total reads, each adjacent four lines contains the information of one read, and the total read number of each file is calculated; total base: the number of all bases in total data; clean reads: filter the original data, remove the linker sequence, remove the contaminated part, and remove the sequence containing more low-quality bases to obtain clean reads; GC%: the percentage of G and C in all bases; error rate: the error rate of sequencing; Q20, Q30: the percentage of total number of bases where the Phred score is greater than 20 and 30 which indicates base call accuracy.