Filename	Name	Sample	Genome	Paired/Single-ended	Read length	Read count from sequencer	Read count successfully aligned	Read count after filtering for mapping quality	Read count after removing duplicate reads	Read count after removing mitochondrial reads (final read count)	Mapping quality > q30 (out of total)		Duplicates (after filtering)		Mitochondrial reads (out of total)		Duplicates that are mitochondrial (out of all dups)		Final reads (after all filters)		NRF	PBC1	PBC2	picard_est_library_size	Fraction of reads in NFR	NFR / mono-nuc reads	Presence of NFR peak	Presence of Mono-Nuc peak	Presence of Di-Nuc peak	Raw peaks	Naive overlap peaks	IDR peaks	Min size	25 percentile	50 percentile (median)	75 percentile	Max size	Mean	Min size	25 percentile	50 percentile (median)	75 percentile	Max size	Mean	Min size	25 percentile	50 percentile (median)	75 percentile	Max size	Mean	TSS_enrichment	Fraction of reads in universal DHS regions		Fraction of reads in blacklist regions		Fraction of reads in promoter regions		Fraction of reads in enhancer regions		Fraction of reads in called peak regions	
./A431-2-CTRLi/qc/rep1/A431-2-CTRLi_S10_L001_R1_001.trim.PE2SE_qc.txt	A431-2-CTRLi_S10_L001_R1_001.trim.PE2SE	A431-2-CTRLi_S10_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	1475666	1463981	1307320	1293397	1272404	1307320	0.885918629283	13923.0	0.021416	91480	0.0624871497649	9970	0.279616333857	1272404	0.862257448501	0.982103 - OK	0.9822 - OK	56.505276 - OK	138343123	0.273098123548 out of range [0.4, inf]	1.46090820654 out of range [2.5, inf]	OK	OK	OK	11919 - OK	115476 - OK	11919 - OK	150.0	573.0	765.0	985.0	4651533.0	8637.22694857	150.0	216.0	449.0	937.0	20171661.0	19507.142298	150.0	573.0	765.0	985.0	4651533.0	8637.22694857	10.3701103504	967994	0.786074378689	1673	0.00135858531721	394117	0.320048756403	619710	0.503245013107	303952	0.246828884839
./A431-2-p63i/qc/rep1/A431-2-p63i_S11_L001_R1_001.trim.PE2SE_qc.txt	A431-2-p63i_S11_L001_R1_001.trim.PE2SE	A431-2-p63i_S11_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	1645900	1630372	1480534	1465303	1441338	1480534	0.899528525427	15231.0	0.020697	39137	0.0240049510173	2344	0.0678279993055	1441338	0.875714198919	0.980696 - OK	0.980855 - OK	52.688735 - OK	338548352	0.290774982966 out of range [0.4, inf]	1.54400160609 out of range [2.5, inf]	OK	OK	OK	20413 - OK	109821 - OK	20413 - OK	150.0	567.0	773.0	1011.0	4316522.0	7859.31269289	150.0	229.0	483.0	976.0	21006678.0	20541.7232497	150.0	567.0	773.0	1011.0	4316522.0	7859.31269289	18.5192033492	1168361	0.820867912014	2381	0.00167284469313	567115	0.398444064739	629510	0.442281588732	550702	0.386912607389
./CAL27-2-p63i/qc/rep1/CAL27-2-p63i_S13_L001_R1_001.trim.PE2SE_qc.txt	CAL27-2-p63i_S13_L001_R1_001.trim.PE2SE	CAL27-2-p63i_S13_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	1909196	1894747	1729528	1714085	1687342	1729528	0.905893370822	15443.0	0.017975	16326	0.00861645380623	562	0.01642314436	1687342	0.883797158595	0.982889 - OK	0.983073 - OK	59.728686 - OK	385560111	0.354554406696 out of range [0.4, inf]	1.93741770583 out of range [2.5, inf]	OK	OK	OK	17522 - OK	148947 - OK	17522 - OK	150.0	530.0	735.0	978.0	3788612.0	7347.71327474	150.0	233.0	464.0	1003.0	21006912.0	14904.0778532	150.0	530.0	735.0	978.0	3788612.0	7347.71327474	19.6532729827	1334322	0.794673518029	2654	0.00158062560375	540712	0.322028346442	825992	0.491930709757	476972	0.284067127156
./CAL27-2-CTRLi/qc/rep1/CAL27-2-CTRLi_S12_L001_R1_001.trim.PE2SE_qc.txt	CAL27-2-CTRLi_S12_L001_R1_001.trim.PE2SE	CAL27-2-CTRLi_S12_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	2505574	2491707	2260026	2233679	2196288	2260026	0.901999302355	26347.0	0.02343	45385	0.0182144208769	3268	0.0548856269524	2196288	0.876560819996	0.977892 - OK	0.978067 - OK	45.976286 - OK	421039660	0.336339585509 out of range [0.4, inf]	1.57253501898 out of range [2.5, inf]	OK	OK	OK	18725 - OK	458643 - OK	18725 - OK	150.0	475.0	734.0	984.0	2373.0	734.915514019	150.0	150.0	190.0	319.0	2386.0	279.730210643	150.0	475.0	734.0	984.0	2373.0	734.915514019	14.2785098971	1522663	0.700233984178	2256	0.00103747701777	589135	0.270928201624	1037905	0.477306109985	510860	0.234931520079
./SCC13-2-p63i/qc/rep1/SCC13-2-p63i_S15_L001_R1_001.trim.PE2SE_qc.txt	SCC13-2-p63i_S15_L001_R1_001.trim.PE2SE	SCC13-2-p63i_S15_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	1691672	1662801	1484866	1465886	1438048	1484866	0.8777505332	18980.0	0.025718	9814	0.00590208930594	286	0.00637396924448	1438048	0.850074955429	0.975116 - OK	0.97532 - OK	40.812073 - OK	143650683	0.230646894831 out of range [0.4, inf]	1.05298620824 out of range [2.5, inf]	OK	OK	OK	5908 out of range [10000, inf]	187545 - OK	5908 out of range [10000, inf]	150.0	490.0	702.0	941.25	1179965.0	7099.46360867	150.0	150.0	354.0	862.0	19560423.0	12066.3653523	150.0	490.0	702.0	941.25	1179965.0	7099.46360867	12.4815230731	947589	0.660981019943	12067	0.00841721249154	335744	0.234194794958	709417	0.494846576126	122564	0.0854932652535
./SCC13-2-CTRLi/qc/rep1/SCC13-2-CTRLi_S14_L001_R1_001.trim.PE2SE_qc.txt	SCC13-2-CTRLi_S14_L001_R1_001.trim.PE2SE	SCC13-2-CTRLi_S14_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	1629252	1612781	1449840	1434464	1411898	1449840	0.889880755095	15376.0	0.021316	28857	0.0178926959085	1350	0.0384462037934	1411898	0.866592767724	0.979645 - OK	0.979828 - OK	50.030573 - OK	226062849	0.25699291398 out of range [0.4, inf]	1.20598653362 out of range [2.5, inf]	OK	OK	OK	5776 out of range [10000, inf]	200262 - OK	5776 out of range [10000, inf]	150.0	468.0	668.0	916.0	1762511.0	9520.53081717	150.0	150.0	337.0	777.0	20156947.0	11370.4464152	150.0	468.0	668.0	916.0	1762511.0	9520.53081717	9.42959371613	877723	0.627639887018	5867	0.00419535914763	269764	0.192902141657	715965	0.511970395795	115988	0.0829403982981