Table 1.

Assembly and annotation statistics of de novo assemblies from short read transcriptome data of ergot susceptible DH372 and ergot moderate resistant Helltop of rye hybrids.

Attributes	Ergot susceptible DH372							Ergot resistant Helltop
	Control			Claviceps purpurea inoculated				Control			Claviceps purpurea inoculated
	ID_1A	ID_2A	ID_3A	ID_4A	ID_5A	ID_6A	Combined DH372	ID_10A	ID_11A	ID_12A	ID_13A	ID_14A	ID-15A	Combined Helltop
Clean reads	24,833,832	24,427,226	24,635,234	18,116,390	20,833,628	24,898,586	137,744,896	24,674,052	24,427,654	26,642,152	24,503,442	25,138,406	24,792,620	150,178,326
Assembled bases	2,483,383,200	2,442,722,600	2,463,523,400	1,811,639,000	2,083,362,800	2,489,858,600	13,774,489,600	2,467,405,200	2,442,765,400	2,664,215,200	2,450,344,200	2,513,840,600	2,479,262,000	15,017,832,600
GC %	52.54	52.77	52.42	50.89	50.46	50.23	51.5	52.2	51	50.97	51.26	50.73	51.78	51.32
Transcript number after Trinity assembly	88,023	84,932	89,825	93,016	91,345	89,342	240,689	92,491	90,991	98,494	88,034	82,404	87,345	248,337
Transcript number after CD-HIT-EST	57,143	47,329	50,616	77,315	62,145	61,134	208,690	53,803	61,158	78,418	58,602	53,529	61,232	192,162
Coding sequences (Rye specific)	36,256	31,603	32,609	42,610	31,235	32,342	66,350	34,888	31,731	43,940	35,299	28,529	32,234	57,965
Rye Unigenes	14,978	13,659	13,951	15,347	13,182	13,092	18,458	14,625	13,478	15,316	14,572	9,358	14,765	18,786
Average contig length	723	694	722	737	743	726	766	722	745	869	802	765	863	787
N50	888	834	900	927	908	899	1220	856	875	998		905	723	1235