Table 2.

Comparison of nuclear and cytoplasmic chromosomes.

		Total Reads
Chr		In ChIP	In input	ChIP/input ratio
	Specific Reads	2356286	441471	5.3373
1-22, X	Noise Reads	24285371	22585024	1.0753
	E(background	4959671
	noise) in ChIP*	(0.2042)
M		89835	409136	0.2196

*Assuming that reads mapped to mitochondrial chromosomes (M) are due to the experimental procedure and not to the non-specific binding of STAT1, the ChIP/input ratio for this background noise is 21.96%. Among chromosome 1-22 and X, the expected background noise in ChIP would be 22585024*0.2196 = 4959671, which accounts for 20.42% of total noise reads.