Table 2.

Summary of Illumina sequencing and mapping of the sequencing read to the genes in the high confidence gene set

	Total reads	Total mapped reads	% mapped readsa	# uniquely mapped reads	% uniquely mapped readsb
520 leaves WW	208,238,566	85,078,408	40.86	84,848,522	99.73
520 roots WW	177,073,828	70,448,906	39.79	70,245,780	99.71
520 leaves drought	223,031,526	111,012,324	49.77	110,732,434	99.75
520 roots drought	170,916,478	70,687,714	41.36	70,463,550	99.68
592 leaves WW	202,996,992	96,790,050	47.68	96,548,610	99.75
592 roots WW	185,878,236	90,739,420	48.82	90,492,450	99.73
592 leaves drought	234,211,410	63,601,116	27.16	63,220,510	99.40
592 roots drought	178,929,458	52,870,112	29.55	52,564,102	99.42
Total	1,581,276,494	641,228,050	40.55	639,115,958	99.67

^aRelative to the total number of reads

^bRelative to the number of mapped reads