Table 3.

Quality control of sequencing data.

Sample	“85-74”	“BJN3-1”	R-pool	S-pool
Raw reads	250,343,998	249,577,324	250,291,386	249,507,094
Raw bases	37,551,599,700	37,436,598,600	37,543,707,900	37,426,064,100
Clean reads	243,624,928	243,358,774	244,980,058	243,367,696
Clean bases	36,543,739,200	36,503,816,100	36,747,008,700	36,505,154,400
Clean read rate (%)	97.32	97.51	97.88	97.54
Low-quality reads	4,481,482	4,157,506	3,183,920	3,906,490
Low-quality read rate (%)	1.79	1.67	1.27	1.57
Ns reads	68,718	70,224	1,542	70,616
Ns read rate (%)	0.03	0.03	0	0.03
Adapter-polluted reads	2,168,870	1,990,820	2,125,866	2,162,292
Adapter-polluted read rate (%)	0.87	0.8	0.85	0.87
Raw Q30 base rate (%)	89.09	89.46	91.68	89.9
Clean Q30 base rate (%)	90	90.3	92.34	90.71