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	
./CAL27-2-p63i-50k/qc/rep1/CAL27-2-p63i-50k_S20_L001_R1_001.trim.PE2SE_qc.txt	CAL27-2-p63i-50k_S20_L001_R1_001.trim.PE2SE	CAL27-2-p63i-50k_S20_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	443928	440484	402366	402053	398562	402366	0.906376709737	313.0	0.001568	7574	0.0171947221693	134	0.176781002639	398562	0.897807752609	0.998611 - OK	0.998614 - OK	723.345588 - OK	126879027	0.24271067153 out of range [0.4, inf]	2.45280009452 out of range [2.5, inf]	OK	OK	OK	68 out of range [10000, inf]	50127 - OK	68 out of range [10000, inf]	219.0	524.0	664.0	771.0	391443.0	12275.3088235	150.0	221.0	401.0	1776.0	20202759.0	49479.0004588	219.0	524.0	664.0	771.0	391443.0	12275.3088235	25.9637808035	321341	0.815486945753	1117	0.00283468003898	126331	0.320597998213	196093	0.497637343674	2075	0.00526585593633
./A431-2-CTRLi-50k/qc/rep1/A431-2-CTRLi-50k_S17_L001_R1_001.trim.PE2SE_qc.txt	A431-2-CTRLi-50k_S17_L001_R1_001.trim.PE2SE	A431-2-CTRLi-50k_S17_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	349130	345560	310526	310147	307452	310526	0.88942800676	379.0	0.002459	17462	0.0505324690358	718	0.671028037383	307452	0.880623263541	0.99904 - OK	0.999046 - OK	1054.340426 - OK	80039068	0.181819026183 out of range [0.4, inf]	1.70191123412 out of range [2.5, inf]	OK	OK	OK	58 out of range [10000, inf]	39766 - OK	58 out of range [10000, inf]	189.0	495.0	666.0	818.0	112667.0	3469.62068966	150.0	213.0	391.0	1110.75	20432809.0	60848.7534829	189.0	495.0	666.0	818.0	112667.0	3469.62068966	24.0219737056	231705	0.778562932199	740	0.00248650900855	93179	0.313095166092	145443	0.488709905042	1631	0.00548040026075
./SCC13-2-CTRLi-50k/qc/rep1/SCC13-2-CTRLi-50k_S21_L001_R1_001.trim.PE2SE_qc.txt	SCC13-2-CTRLi-50k_S21_L001_R1_001.trim.PE2SE	SCC13-2-CTRLi-50k_S21_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	318034	313510	278290	278013	275668	278290	0.875032229259	277.0	0.002006	13923	0.0444100666645	514	0.589449541284	275668	0.866787827717	0.999097 - OK	0.999111 - OK	1143.196581 - OK	93007788	0.173486298025 out of range [0.4, inf]	1.64495657983 out of range [2.5, inf]	OK	OK	OK	12 out of range [10000, inf]	30646 - OK	12 out of range [10000, inf]	150.0	172.5	284.5	18753.0	185502.0	29861.25	150.0	192.0	321.0	4791.25	20174902.0	81488.4312798	150.0	172.5	284.5	18753.0	185502.0	29861.25	15.9218112456	171218	0.639488761569	1511	0.00564349261603	53820	0.201014409394	133634	0.49911481949	83	0.000309999925301
./SCC13-2-p63i-50k/qc/rep1/SCC13-2-p63i-50k_S22_L001_R1_001.trim.PE2SE_qc.txt	SCC13-2-p63i-50k_S22_L001_R1_001.trim.PE2SE	SCC13-2-p63i-50k_S22_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	381160	375444	334418	334131	331410	334418	0.877369083849	287.0	0.001729	7791	0.0207514303065	188	0.219114219114	331410	0.869477384825	0.998601 - OK	0.998635 - OK	748.614679 - OK	102476208	0.208561311677 out of range [0.4, inf]	2.04228664466 out of range [2.5, inf]	OK	OK	OK	12 out of range [10000, inf]	40118 - OK	12 out of range [10000, inf]	150.0	337.75	575.0	746.5	414005.0	34984.9166667	150.0	198.0	329.0	5917.5	20363794.0	64112.8584675	150.0	337.75	575.0	746.5	414005.0	34984.9166667	17.2677330567	216914	0.663641870682	2672	0.00817490377967	71520	0.218813292785	161394	0.493780097536	329	0.00100656562257
./A431-2-p63i-50k/qc/rep1/A431-2-p63i-50k_S18_L001_R1_001.trim.PE2SE_qc.txt	A431-2-p63i-50k_S18_L001_R1_001.trim.PE2SE	A431-2-p63i-50k_S18_L001_R1_001.trim.PE2SE	hg19	Paired-ended	75	387708	383382	345184	344935	342224	345184	0.890319518813	249.0	0.001453	8289	0.0216207333678	196	0.303405572755	342224	0.882684907198	0.998923 - OK	0.998921 - OK	926.186813 - OK	151808073	0.197889070854 out of range [0.4, inf]	1.86386900121 out of range [2.5, inf]	OK	OK	OK	102 out of range [10000, inf]	41188 - OK	102 out of range [10000, inf]	150.0	463.5	571.0	776.25	78305.0	3295.38235294	150.0	214.0	394.0	1171.0	20202756.0	58787.7899631	150.0	463.5	571.0	776.25	78305.0	3295.38235294	26.2246009235	242094	0.717349563239	964	0.00285643171232	111809	0.331301632077	139387	0.413018098636	2694	0.00798260065662