Table 2. ABI SOLiD sequencing results of in vivo and in vitro nucleosome occupancy maps.

	In Vivo	In Vitro
Total ends	49.75 M	70.17 M
Paired reads	20.39 M	29.85 M
% paired	40.99%	42.54%
Unique reads	16.59 M	25.29 M
% unique	81.33%	84.71%
# of BACs	6	6
Total bps	924,743	924,743
Reads/bp	3587	5470

We analyzed the results of the sequencing run in the following manner. First, we defined paired reads for pairs where each end aligned to the same chromosome. From that subset, we removed alignment scores that were not unique as assigned by bowtie. Finally we estimated the sequencing coverage (Reads/bp) by multiplying the number of reads by the average length in bp of each read, then dividing by the number of bps each BAC pool contained.