Table 1.

Properties of the different libraries; abbreviations are as follows: COT cotyledons, E etiolated leaves, L light treated etiolated leaves, EPI epicotyl, LVN.1-5 leaf libraries 1-5, FLO flower, HYP hypocotyl, LVR.1 leaf library, non normalized; ^asequenced with GS flex, ^bsequenced with GS 20; all libraries were normalized except LVR.1;

library	number of raw reads	number of reads after crossmatch clean up	number of reads after MIRA	number reads for the assembly	number of reads with AGI mapping	raw nts	nts after crossmatch	mean readlength raw	mean read length after crossmatch
COTa	343,694	335,050	272,731	272402	220,875	81,050,491	75,679,454	235	225
Ea	144,290	135,906	120,202	120126	101,119	34,849,428	32,229,999	241	237
La	192,117	174,563	157,977	157921	137,359	46,654,732	41,408,162	242	237
EPIa	243,294	233,143	189,093	188193	148,059	54,072,084	50,193,810	222	215
LVN.5a	320,209	311,538	268,315	267966	223,735	77,473,643	72,627,353	241	233
sum/averagea						294,100,378	272,138,778	236	228
LVN.1b	350,016	343,361	278,080	277888	228,894	36,551,286	33,767,205	104	98
LVN.2b	302,341	295,416	234,029	233790	192,903	31,399,731	29,009,144	103	98
LVN.3b	146,504	142,862	115,832	115751	96,087	15,049,571	13,963,252	102	97
LVN.4b	278,936	272,367	223,939	223596	184,175	28,590,490	26,562,093	102	97
FLOb	162,353	153,765	95,229	95097	70,957	17,047,889	15,039,288	105	97
HYPb	349,976	327,769	255,437	255310	210,073	36,269,788	31,823,328	103	97
sum/averageb						164,908,755	150,164,310	103	97
LVR.1b	308,042	293,201	191,394	191205	167,551	27,779,787	24,062,060	90	82
total	3,141,772	3,018,941	2,402,258	2399245		486,788,920	446,365,148