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	
./A431-1-p63i-50k/qc/rep1/A431-1-p63i-50k_S8_L001_R1_001.trim.PE2SE_qc.txt	A431-1-p63i-50k_S8_L001_R1_001.trim.PE2SE	A431-1-p63i-50k_S8_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1064708	483766	326781	326582	321770	326781	0.306920770765	199.0	0.001235	21714	0.0448853371258	4972	0.2159485754	321770	0.302214316038	0.998984 - OK	0.998995 - OK	1006.872611 - OK	1671295	0.138575061302 out of range [0.4, inf]	1.09257226054 out of range [2.5, inf]	OK	OK	OK	85 out of range [10000, inf]	48158 - OK	85 out of range [10000, inf]	150.0	559.0	706.0	845.0	403663.0	11121.3764706	150.0	150.0	328.0	732.0	20529311.0	49598.5576021	150.0	559.0	706.0	845.0	403663.0	11121.3764706	21.6405159184	243415	0.769137191211	841	0.00265737270837	110068	0.347790367735	140449	0.443787561853	2336	0.00738123977022
./SCC13-1-CTRLi-500k/qc/rep1/SCC13-1-CTRLi-500k_S17_L001_R1_001.trim.PE2SE_qc.txt	SCC13-1-CTRLi-500k_S17_L001_R1_001.trim.PE2SE	SCC13-1-CTRLi-500k_S17_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1177746	558066	375423	374938	369808	375423	0.318763977971	485.0	0.002616	40069	0.0717997512839	6804	0.246611090975	369808	0.313996396507	0.999071 - OK	0.999076 - OK	1087.484663 - OK	1813140	0.169365343614 out of range [0.4, inf]	1.30469215799 out of range [2.5, inf]	OK	OK	OK	12 out of range [10000, inf]	49882 - OK	12 out of range [10000, inf]	150.0	511.25	618.0	6792.0	354399.0	38389.25	150.0	150.0	305.0	853.75	20203263.0	51015.5662764	150.0	511.25	618.0	6792.0	354399.0	38389.25	12.3042198402	229256	0.64606817567	1718	0.00484150960411	60439	0.170323631527	188595	0.531481084859	151	0.000425534313283
./SCC13-1-p63i-50k/qc/rep1/SCC13-1-p63i-50k_S12_L001_R1_001.trim.PE2SE_qc.txt	SCC13-1-p63i-50k_S12_L001_R1_001.trim.PE2SE	SCC13-1-p63i-50k_S12_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	952048	378458	225586	225410	221138	225586	0.236948137069	176.0	0.001589	24032	0.063499780689	5358	0.219788333744	221138	0.232276103726	0.999033 - OK	0.999116 - OK	1205.955056 - OK	1257514	0.123766487422 out of range [0.4, inf]	1.13173706936 out of range [2.5, inf]	OK	OK	OK	6 out of range [10000, inf]	27209 - OK	6 out of range [10000, inf]	150.0	173.0	265.0	605.25	26629.0	4695.0	150.0	150.0	295.0	963.0	20202700.0	89075.7888199	150.0	173.0	265.0	605.25	26629.0	4695.0	17.6275960734	153973	0.716613454217	1694	0.00788413027897	54285	0.252650538485	107427	0.4999813834	99	0.000460760860459
./CAL27-1-p63i-50k/qc/rep1/CAL27-1-p63i-50k_S10_L001_R1_001.trim.PE2SE_qc.txt	CAL27-1-p63i-50k_S10_L001_R1_001.trim.PE2SE	CAL27-1-p63i-50k_S10_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1174456	656127	499886	499489	492940	499886	0.425631952155	397.0	0.001608	17285	0.0263439852346	4400	0.204024853937	492940	0.419717724632	0.998568 - OK	0.998566 - OK	696.264957 - OK	2286247	0.229481637116 out of range [0.4, inf]	1.89886616274 out of range [2.5, inf]	OK	OK	OK	135 out of range [10000, inf]	69775 - OK	135 out of range [10000, inf]	150.0	400.0	524.0	746.0	435210.0	6920.83703704	150.0	197.0	341.0	829.0	20203999.0	35144.9348907	150.0	400.0	524.0	746.0	435210.0	6920.83703704	20.1123684954	372860	0.76179385024	1161	0.0023720502605	128177	0.261879660844	253258	0.517433854326	3350	0.00684441720298
./A431-1-CTRLi-50k/qc/rep1/A431-1-CTRLi-50k_S7_L001_R1_001.trim.PE2SE_qc.txt	A431-1-CTRLi-50k_S7_L001_R1_001.trim.PE2SE	A431-1-CTRLi-50k_S7_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1246674	433457	227339	227112	222208	227339	0.182356413946	227.0	0.002039	34543	0.0796918725502	8266	0.222755201035	222208	0.178240662755	0.999062 - OK	0.999117 - OK	1209.25 - OK	1218436	0.11097000563 out of range [0.4, inf]	0.974294869032 out of range [2.5, inf]	OK	OK	OK	5 out of range [10000, inf]	32153 - OK	5 out of range [10000, inf]	324.0	549.0	714.0	714.0	782.0	616.6	150.0	150.0	305.0	738.0	20432870.0	74981.8935714	324.0	549.0	714.0	714.0	782.0	616.6	19.0123824087	158740	0.745209235074	438	0.00205620287868	65683	0.308350624842	100217	0.470471424413	130	0.000610288525637
./CAL27-1-CTRLi-500k/qc/rep1/CAL27-1-CTRLi-500k_S15_L001_R1_001.trim.PE2SE_qc.txt	CAL27-1-CTRLi-500k_S15_L001_R1_001.trim.PE2SE	CAL27-1-CTRLi-500k_S15_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1294162	668823	487130	486730	481144	487130	0.376405735913	400.0	0.00166	29461	0.0440490234337	6104	0.225106947927	481144	0.371780348983	0.998882 - OK	0.998906 - OK	931.071146 - OK	2125929	0.202781890291 out of range [0.4, inf]	1.51596582647 out of range [2.5, inf]	OK	OK	OK	111 out of range [10000, inf]	70103 - OK	111 out of range [10000, inf]	150.0	487.5	618.0	741.5	683011.0	10072.1531532	150.0	155.0	332.0	797.5	20174943.0	34960.3963454	150.0	487.5	618.0	741.5	683011.0	10072.1531532	14.5335240118	342073	0.725305644727	824	0.00174714710385	93061	0.197319486203	265918	0.563832358691	2862	0.00606836773206
./CAL27-1-CTRLi-50k/qc/rep1/CAL27-1-CTRLi-50k_S9_L001_R1_001.trim.PE2SE_qc.txt	CAL27-1-CTRLi-50k_S9_L001_R1_001.trim.PE2SE	CAL27-1-CTRLi-50k_S9_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	826802	494548	385699	385431	381062	385699	0.466495001222	268.0	0.001405	19208	0.0388395059731	2664	0.236968510941	381062	0.46088664517	0.999038 - OK	0.99908 - OK	1111.267857 - OK	2200517	0.171573839357 out of range [0.4, inf]	1.35196895332 out of range [2.5, inf]	OK	OK	OK	27 out of range [10000, inf]	56669 - OK	27 out of range [10000, inf]	150.0	448.0	638.0	714.5	55432.0	2628.03703704	150.0	150.0	317.0	775.0	20174770.0	43243.0151935	150.0	448.0	638.0	714.5	55432.0	2628.03703704	16.371089068	269208	0.720354493787	833	0.00222896531056	83456	0.223313960334	199403	0.533568271094	581	0.00155465647711
./A431-1-p63i-500k/qc/rep1/A431-1-p63i-500k_S14_L001_R1_001.trim.PE2SE_qc.txt	A431-1-p63i-500k_S14_L001_R1_001.trim.PE2SE	A431-1-p63i-500k_S14_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1113826	476463	309043	308786	304432	309043	0.277460752398	257.0	0.001686	26900	0.0564576892644	6134	0.222407541697	304432	0.273320967548	0.998917 - OK	0.998963 - OK	1002.777027 - OK	1560515	0.139448343649 out of range [0.4, inf]	1.12040818845 out of range [2.5, inf]	OK	OK	OK	96 out of range [10000, inf]	44279 - OK	96 out of range [10000, inf]	150.0	521.0	577.5	749.0	1714633.0	33463.71875	150.0	157.0	343.0	783.0	20171923.0	54521.078299	150.0	521.0	577.5	749.0	1714633.0	33463.71875	22.1911176181	236251	0.795104532666	597	0.00200920802875	98095	0.330139466634	143778	0.483885949679	2692	0.00905994642112
./SCC13-1-CTRLi-50k/qc/rep1/SCC13-1-CTRLi-50k_S11_L001_R1_001.trim.PE2SE_qc.txt	SCC13-1-CTRLi-50k_S11_L001_R1_001.trim.PE2SE	SCC13-1-CTRLi-50k_S11_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	553636	543917	483852	482711	477406	483852	0.873953283385	1141.0	0.004757	35335	0.0649639558977	2580	0.734624145786	477406	0.862310254391	0.99857 - OK	0.998594 - OK	716.949686 - OK	55501059	0.206335149218 out of range [0.4, inf]	1.57782195852 out of range [2.5, inf]	OK	OK	OK	22 out of range [10000, inf]	67822 - OK	22 out of range [10000, inf]	150.0	374.75	552.5	608.5	117880.0	9404.31818182	150.0	150.0	301.0	752.0	20168332.0	37271.3490755	150.0	374.75	552.5	608.5	117880.0	9404.31818182	13.5566504582	291559	0.638501631518	2623	0.00574425683814	85216	0.186619363599	230490	0.504763156166	436	0.000954821190023
./SCC13-1-p63i-500k/qc/rep1/SCC13-1-p63i-500k_S18_L001_R1_001.trim.PE2SE_qc.txt	SCC13-1-p63i-500k_S18_L001_R1_001.trim.PE2SE	SCC13-1-p63i-500k_S18_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	1127678	495724	321699	321409	316454	321699	0.285275583988	290.0	0.001829	26640	0.0537395808958	6450	0.221360422816	316454	0.280624433571	0.998554 - OK	0.998597 - OK	728.731132 - OK	1600381	0.159944567948 out of range [0.4, inf]	1.40513409246 out of range [2.5, inf]	OK	OK	OK	10 out of range [10000, inf]	43719 - OK	10 out of range [10000, inf]	249.0	288.5	339.5	664.0	220001.0	37406.3	150.0	150.0	297.0	799.0	20174935.0	58342.1630412	249.0	288.5	339.5	664.0	220001.0	37406.3	15.3378536126	219178	0.708360265791	2503	0.00808943299635	68759	0.222221863123	162793	0.526129870466	157	0.000507407503167
./A431-1-CTRLi-500k/qc/rep1/A431-1-CTRLi-500k_S13_L001_R1_001.trim.PE2SE_qc.txt	A431-1-CTRLi-500k_S13_L001_R1_001.trim.PE2SE	A431-1-CTRLi-500k_S13_L001_R1_001.trim.PE2SE	hg19	Paired-ended	50	989728	493279	356983	356236	351916	356983	0.360687987002	747.0	0.004227	47223	0.0957328408467	5258	0.293611793612	351916	0.35556839859	0.998771 - OK	0.9988 - OK	853.911917 - OK	1872493	0.141135567406 out of range [0.4, inf]	1.04557067512 out of range [2.5, inf]	OK	OK	OK	48 out of range [10000, inf]	51657 - OK	48 out of range [10000, inf]	150.0	536.5	683.0	864.25	1218620.0	29723.3541667	150.0	150.0	316.0	721.0	20204077.0	46829.7343051	150.0	536.5	683.0	864.25	1218620.0	29723.3541667	17.3169361739	244516	0.740921652284	527	0.00159689227189	92220	0.2794409968	164778	0.499303064094	1554	0.0047088626006