Online Supplementary Information: Nature : This file contains the details of computational methods, supplementary figures and tables.

Raw sequence data and alignment results: GEO-GSE36063

Combined cleavage frequency and NCP score: combinedData_cor.tgz: This file contains the cleavage frequency on both strands from the six indepedent experiments. It also contains the NCP score and the NCP score/noise ratio from the Bayesian deconvolution at every genomic location(unmappable regions are skipped in this analysis).

Statistical details for deconvolution of nucleosome positioning signals of chemical data:

Xi, L., Brogaard, K.,Zhang, Q., Lindsay, B., Widom, J. and Wang, J.-P., A locally convoluted cluster model for nucleosome positioning signals in chemical map, Journal of American Statistical Association , 2014, 109(505) 48-62

Errata: In Supplementary Tables 2 and 3 published with the paper online, the nucleosome positions on Chromosome 10 after coordinate 126894 were systematically shifted by one base pair because of genome version issue used in the alignment. Here are the corrected tables:

• Supplementary Table 2
This file contains a list of nucleosomes in the unique map with NCP score and NCP score/noise ratio. Tab delimited text file. The names of the four columns are: chromosome ID, position, NCP score and NCP score/noise ratio.

• Supplementary Table 3
This file contains a list of nucleosomes in the redundant map with NCP score and NCP score/noise ratio. Tab delimited text file. The names of the four columns are: chromosome ID, position, NCP score and NCP score/noise ratio.

R package based on Poisson deconvolution algorithm

     NuCMap R package manual: NuCMap-manual.pdf
     Source package for all platforms: NuCMap_1.0.tar.gz
     Binary package for Mac OS X 10.9 or above: NuCMap_1.0.tgz
     Binary package for Windows 7: NuCMap_1.0.zip