Table 1. Read quality and mapping results for the RNA-Seq libraries.

Sample	NCBI BioSample	Treatment	Total reads	Cleaned reads	Mapped to Cyprinus carpio genome	Mapped to CyHV-3 genome
1	SAMN04537393	Acute	28,645,158	25,048,054	18,741,223 (74.8%)	360,418 (1.4389%)
2	SAMN04537394	Acute	31,309,358	28,452,933	21,568,752 (75.8%)	5,434 (0.0191%)
3	SAMN04537395	Acute	33,802,985	30,992,654	23,530,831 (75.9%)	5,337 (0.0172%)
4	SAMN04537396	Persistent	33,014,462	30,415,615	23,004,950 (75.6%)	96 (0.0003%)
5	SAMN04537397	Persistent	32,699,016	30,139,958	22,157,303 (73.5%)	101 (0.0003%)
6	SAMN04537398	Persistent	31,940,121	29,333,923	22,088,110 (75.3%)	66 (0.0002%)
7	SAMN04537399	Reactivated	33,243,586	30,521,918	22,959,764 (75.2%)	407 (0.0013%)
8	SAMN04537400	Reactivated	33,933,720	31,064,624	23,427,770 (75.4%)	261 (0.0008%)
9	SAMN04537401	Reactivated	32,050,049	28,934,613	21,425,596 (74.0%)	9,059 (0.0313%)
10	SAMN04537403	Mock	31,401,721	28,838,999	20,698,717 (71.8%)	95 (0.0003%)
11	SAMN04537404	Mock	36,074,985	32,918,417	24,248,317 (73.7%)	39 (0.0001%)

^*Cyprinus carpio genome is from www.carpbase.org and the CyHV-3 genome is GenBank #DQ657948.1.