Table 4. The 20 most abundant E. festucae transcripts found in the endophyte-infected plant S1139RC.

	Mapped match	Gene identification	Mean % mapped tags
1	SRR493691.19548	NC12 (epichloae specific)	10.12
2	SRR493691.12929	Secreted, Antifungal protein (small, cysteine-rich)	6.34
3	SRR493690.59639	Secreted, Unknown function (small, cysteine-rich)	4.60
4	SRR493691.55163	Secreted, Subtilisin-like protease	2.60
5	SRR493691.16186	Unknown function (epichloae specific)	2.58
6	SRR493691.34496	Secreted, Unknown function (epichloae specific)	1.90
7	SRR493691.15406	Secreted, NC25 (gigA) (epichloae specific)	1.45
8	SRR493691.46417	Secreted, Conidiation associated	1.37
9	SRR493691.19548	Antisense, NC12 (epichloae specific)	1.17
10	SRR493691.31334	Unknown function (epichloae specific)	1.14
11	SRR493691.38494	Unknown function, glucose repressible Grg1	1.04
12	SRR493690.32961	Secreted, Unknown function	1.02
13	SRR493691.32405	Secreted, Unknown function (small, cysteine-rich) (epichloae specific)	1.01
14	SRR493691.6870	Secreted, Unknown function (small, cysteine-rich) (epichloae specific)	0.97
15	AFRX01000547	Secreted, Unknown function (small, cysteine-rich)	0.87
16	SRR493691.52692	Unknown function (epichloae specific)	0.84
17	SRR493691.35651	Secreted, Unknown function (epichloae specific)	0.76
18	SRR493691.71157	Mismatched base pair and cruciform DNA recognition protein	0.62
19	SRR493691.48167	Secreted, Unknown function (small, cysteine-rich) (epichloae specific)	0.62
20	SRR493691.69494	Secreted, Unknown function, RNase domain	0.61