Table 3. Summary of mRNA expression libraries.

libraries	RSV-infected			Mock-inoculated
	RI-1	RI-2	RI-3	CK-1	CK-2	CK-3
Total Reads	14,835,261	14,492,224	14,732,837	14,881,310	14,669,472	14,549,952
Clean Reads	12,320,457 (83.05%)	12,017,087 (82.92%)	12,184,656 (82.70%)	12,536,406 (84.24%)	12,564,718 (85.65%)	12,904,497 (88.69%)
Gene Mapped Reads	7,909,384 (64.20%)	7,673,824 (63.86%)	7,931,898 (65.10%)	7,804,736 (62.26%)	7,679,041 (61.12%)	7,702,403 (59.69%)
Gene Mapped Unique Reads	7,211,957 (91.18%)	7,274,850 (94.80%)	7,435,947 (93.75%)	7,055,951 (90.41%)	7,078,078 (92.17%)	7,121,819 (92.46%)
Reads Perfect Match	3,816,259 (48.25%)	3,612,234 (47.07%)	3,946,378 (49.75%)	3,258,439 (41.74%)	3,916,967 (51.00%)	3,627,663 (47.10%)
No. of Mapped genes	12,863	12,795	12,797	12,531	12,438	12,153

Note

Total Reads: the raw data after sequencing

Clean Reads: the reads after filtering out low-quality tags, unexpected-length tags, and single-copy tags

Gene Mapped Reads: the reads of the clean reads that could be mapped to the rice genome

Reads perfect match: the reads of the gene that could be mapped to the rice genome with 0 mismatch.