Table 3.

Mapping and Peak Processing Statistics.

		Example 1 Low complexity/Sparse read coverage	Example 2 Intermediate complexity/Low background	Example 3 High complexity/High background	Merged Replicates**
Final library concentration (μM)		1.3	6.6	33.9	N/A
Total reads		59,241,310	87,868,338	81,734,480
% Uniquely mapped		62.8716	69.0193	64.6791
non duplicate fraction		0.0757579	0.133552	0.463592
CpGs (coverage ≥ 5)		270,381	1,302,954	2,089,067	3,379,747
Genrich	p-value (< 0.05)				q-value (< 0.05)
	Peaks called	456,542	169,122	80,894	69,886
	FRiP*	0.476	0.428	0.205	0.217
	p-value (<0.01)				q-value (< 0.01)
	Peaks called	34,718	60,870	29,990	50,199
	FRiP*	0.201	0.346	0.137	0.185
	p-value (<0.005)				q-value (< 0.005)
	Peaks called	57,944	73,068	31,091	43,792
	FRiP*	0.174	0.315	0.119	0.173
MACS2 ***	q-value (<0.05) narrowPeak				N/A
	Peaks called	15,322	64,127	76,310
	FRiP*	0.08	0.277	0.131
	q-value (<0.05) broadPeak
	Peaks called	15,294	58,423	64,903
	FRiP*	0.085	0.232	0.138
	q-value (<0.005) narrowPeak
	Peaks called	9,780	63,903	57,829
	FRiP*	0.063	0.243	0.115
	q-value (<0.05) broadPeak
	Peaks called	9,615	55,782	48,217
	FRiP*	0.066	0.267	0.12

^*Fraction of reads in called peak regions. All reads mapping to non-mitochondrial chromosomes (non-chrM) in peak regions are divided by the total number of total non-chrM reads to evaluate the signal to noise ratio in ATAC-seq data. Background descriptions are based on this ratio. Generally, FRiP scores correlate with the number of regions called, and scores ≥ 0.2 are considered acceptable for standard ATAC-seq⁵², although ATAC-Me FRiP scores may differ. We have filtered out mitochondrial reads for this calculation as we do not call peaks on mitochondrial fragments.

^**Genrich can incorporate replicates into peak calling analysis and the resulting merged data is produced using the arguments described in “Data Processing”. MACS2 does not have this option. As a consequence, merged replicate data for MACS2 peaks will depend on the approach chosen for determining consensus peaks.

^***MACS2 has the option of calling “broad” or “narrow” peaks. We provide both here.