Table 3.

Summary of filter data.

Sample name	Raw reads	Raw bases	Clean reads	GC%	Q20 (%)	Q30 (%)	Clean bases	Clean bases%
cont1	67572136	10135820400	65650056	48.57	99.16	97.32	9689017234	95.59
cont2	66474707	9971206050	65006370	47.54	99.22	97.52	9514596643	95.42
infect1	69033293	9854993950	65789887	49.67	98.95	96.74	9383925239	95.22
infect2	70292999	10543949850	68826092	49.91	98.94	96.69	10102208096	95.81

Raw reads: statistics of raw reads, each adjacent four lines contains the information of one read, and the total read number of each file is calculated; raw base: the number of all bases in raw 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; Q20, Q30: the percentage of total number of bases where the Phred score is greater than 20 and 30 which indicates base call accuracy; clean bases: the number and length of sequences in clean reads calculate the number of bases; clean bases%: percentage of clean bases/raw base.