Table 1.

Number of Reads, Filtering, and Mapping of the Two Replicates

	Replicate 1				Replicate 2
	WT	WT_pH	snf1	Snf1_pH	WT	WT_pH	snf1	snfi_pH
Total reads	25,609	43,559	37,296	43,308	28,322	47,040	40,230	47,327
Filtered duplicated reads	4,350	7,106	6,065	6,774	3,003	5,146	4,035	4,442
Non-redundant reads	21,259	36,453	31,231	36,534	25,319	41,894	36,195	42,885
Reads with good quality	20,964	35,740	30,709	35,971	24,326	40,235	34,683	41,412
Number of reads with unique mapping on Ensembl transcripts	7,768	12,450	11,911	13,980	9,119	13,961	14,152	16,188
Number of reads with unique mapping on transcripts as in (Nagalakshmi et al., 2008)	17,525	29,152	25,693	29,004	20,391	32,505	29,111	33,592
Number of reads with no transcript mapping	1,503	2,397	2,398	3,034	1,683	2,987	2,478	3,489
Number of reads with multiple mapping on transcripts	860	1,476	1,146	1,524	942	1,597	1,354	1,580
Number of transcripts with reads	3,564	4,172	4,384	4,770	3,862	4,344	4,552	4,955
Number of undetected transcritps	3,560	2,952	2,740	2,354	3,262	2,780	2,572	2,169