Table 1.

Descriptive summary of data generated by RNA-Seq

Sample ID	Raw reads	Clean reads	Clean ratio	Total reads for alignment (QC-passed reads + QC-failed reads)	Mapped reads (total)	Mapped ratio (total)	Mapped reads (paired)	Mapping ratio (paired)
Infect 1	46,065,300	45,922,764	0.996905784	49,636,717	45,797,615	92.27%	38,974,528	84.87%
Infect 2	55,562,182	55,406,236	0.997193307	59,954,026	55,360,811	92.34%	47,118,286	85.04%
Infect 3	50,507,214	50,357,430	0.997034404	54,364,730	50,035,130	92.04%	42,426,394	84.25%
Infect 4	52,906,558	52,752,936	0.997096352	57,115,291	52,716,642	92.30%	45,013,566	85.33%
Infect 5	59,979,834	59,803,794	0.997065014	64,780,302	59,797,269	92.31%	51,204,340	85.62%
Infect 6	52,050,326	51,879,500	0.996718061	55,819,070	51,276,842	91.86%	43,823,066	84.47%
Mock 1	49,060,712	48,908,052	0.996888345	53,021,565	49,094,574	92.59%	41,888,032	85.65%
Mock 2	50,977,484	50,835,088	0.997206688	55,172,358	51,304,563	92.99%	43,812,718	86.19%
Mock 3	46,718,068	46,578,322	0.997008738	50,307,889	46,715,213	92.86%	40,165,022	86.23%
Mock 4	52,353,214	52,206,814	0.99720361	56,319,798	52,293,923	92.85%	44,864,730	85.94%
Mock 5	47,101,820	46,967,422	0.99714665	50,670,957	47,005,003	92.77%	40,382,898	85.98%
Mock 6	48,607,592	48,462,936	0.997024004	52,119,972	48,147,901	92.38%	41,313,114	85.25%

Mapped ratio (total) Mapped reads (total)/Total reads for alignment (QC-passed reads + QC-failed reads)

Mapping ratio (paired) Mapped reads (paired)/Clean reads