TABLE 1.

The top 20 most expressed annotated genes.

Gene	Presence of promoter	Expression pattern	Predicted function	0 h	1 h	2 h	4 h	5 h	6 h	8 h	10 h	12 h	Total
MAR_ORF300	N	L	–	1349	31	69	36587	49038	50252	55730	67099	58015	318169
MAR_ORF390	Y	L	multiple zinc ribbon protein	1776	9869	27205	51234	49629	43289	39411	45095	50282	317790
MAR_ORF317	N	L	–	1354	170	40	36306	39576	39271	54230	35973	68786	275705
MAR_ORF342	Y	L	major capsid protein	609	48	26	61325	45875	40048	66725	23909	30871	269436
MAR_ORF384	N	L	–	899	134	23	38560	35602	42222	50020	54510	34821	256790
MAR_ORF370	N	L	–	1317	317	948	17200	28825	27160	39832	89992	36077	241669
MAR_ORF219	Y	L	–	793	106	12744	84839	47325	22149	20213	17578	19583	225329
MAR_ORF029	N	I	–	1843	24117	60761	27563	19259	17693	24533	14184	22469	212422
MAR_ORF305	Y	L	–	379	32	28	35828	39222	43383	28499	15090	25099	187560
MAR_ORF413	Y	L	histone H3	520	44	66	16092	35578	41292	29851	22200	25556	171199
MAR_ORF109	Y	L	–	926	260	24676	29570	17876	9340	5808	5875	10734	105065
MAR_ORF421	N	L	–	210	62	1986	17949	17338	21450	21452	9317	15270	105033
MAR_ORF412	N	E	–	54414	40209	5914	197	101	196	130	202	192	101555
MAR_ORF026	Y	L	–	402	179	173	6830	15641	19574	15741	14843	27536	100920
MAR_ORF193	Y	L	–	385	74	2351	13831	16722	14791	16327	15747	17850	98078
MAR_ORF021	Y	L	zinc finger protein	720	77	16	8775	16500	19814	19344	15478	17237	97962
MAR_ORF389	Y	E	–	27733	43921	21364	514	409	534	396	744	438	96053
MAR_ORF250	N	L	–	202	227	94	15714	20837	21501	16581	9799	10734	95689
MAR_ORF014	N	E	–	66374	22286	2559	98	84	17	59	53	62	91592
MAR_ORF147	N	E	–	44432	36392	2414	141	94	117	85	77	58	83810

The total number of normalized reads counts is presented for each gene as well as the read count at each time point of infection. N, no; Y, yes; E, early; I, intermediate; L, late.