Table 1.

RNA-seq read information.

Tissue	Samples	Raw Data	Clean Reads	Mapped	Mapped %	Multiple	Multiple %	Unique	Unique %
spike	L661 spike at 0 HAI	48,619,708	44,064,636	31,413,442	71.3%	7,948,442	25.3%	23,472,782	74.7%
	L693 spike at 0 HAI	54,638,926	50,729,857	37,433,618	73.8%	15,223,441	40.7%	22,210,177	59.3%
	L661 spike at 24 HAI	80,401,044	14,261,236	6,799,856	47.7%	2,277,018	33.5%	4,522,838	66.5%
	L693 spike at 24 HAI	56,001,617	37,706,168	24,971,426	66.2%	7,770,208	31.1%	17,201,218	68.9%
	L661 spike at 72 HAI	64,589,048	47,444,396	29,577,848	62.3%	9,209,005	31.1%	20,368,843	68.9%
	L693 spike at 72 HAI	73,276,052	52,378,107	33,229,807	63.4%	9,061,381	27.3%	24,168,426	72.7%
leaf	L661 leaf at 0 HAI	74,642,980	40,067,567	28,798,631	71.9%	9,266,948	32.2%	19,983,610	69.4%
	L693 leaf at 0 HAI	53,896,907	37,849,318	18,909,880	50.0%	8,498,338	44.9%	10,411,542	55.1%
	L661 leaf at 24 HAI	52,460,707	45,960,283	35,981,574	78.3%	20,792,164	57.8%	15,189,410	42.2%
	L693 leaf at 24 HAI	54,132,118	45,690,464	32,199,399	70.5%	20,182,030	62.7%	12,017,369	37.3%
	L661 leaf at 72 HAI	50,556,369	26,746,381	18,315,598	68.5%	9,430,647	51.5%	6,319,347	34.5%
	L693 leaf at 72 HAI	49,560,263	26,728,939	18,240,700	68.2%	10,006,376	54.9%	8,234,324	45.1%

HAI: Hours after inoculation.