QC Report

	general
Report generated at	2021-08-28 15:48:53
Title	ceh-58_OP808_youngadult_1_2
Description	gevirl
Pipeline version	v1.3.6
Pipeline type	tf
Genome	WS245chr
Aligner	bwa
Sequencing endedness	{'rep1': {'paired_end': True}, 'rep2': {'paired_end': True}, 'ctl1': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	17252530	14656064	16487210
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17063166	14544096	16429861
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.9	99.2	99.7
Paired Reads	17252530	14656064	16487210
Paired Reads (QC-failed)	0	0	0
Read1	8626265	7328032	8243605
Read1 (QC-failed)	0	0	0
Read2	8626265	7328032	8243605
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17005302	14486226	16351500
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.6	98.8	99.2
With itself	17044430	14530212	16419020
With itself (QC-failed)	0	0	0
Singletons	18736	13884	10841
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6548	6446	26952
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7727426	6561358	7516329
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	995658	806368	882830
Paired Optical Duplicate Reads	57932	47161	60254
% Duplicate Reads	12.884699999999999	12.2897	11.7455

Filtered out (samtools view -F 1804):

read unmapped (0x4)
mate unmapped (0x8, for paired-end)
not primary alignment (0x100)
read fails platform/vendor quality checks (0x200)
read is PCR or optical duplicate (0x400)

SAMstat (filtered/deduped BAM)

	rep1	rep2	ctl1
Total Reads	13463536	11509980	13266998
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13463536	11509980	13266998
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	13463536	11509980	13266998
Paired Reads (QC-failed)	0	0	0
Read1	6731768	5754990	6633499
Read1 (QC-failed)	0	0	0
Read2	6731768	5754990	6633499
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13463536	11509980	13266998
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	13463536	11509980	13266998
With itself (QC-failed)	0	0	0
Singletons	0	0	0
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	0	0	0
Diff. Chroms (QC-failed)	0	0	0

Filtered and duplicates removed

Sequence quality metrics (filtered/deduped BAM)

Open chromatin assays are known to have significant GC bias. Please take this into consideration as necessary.

Library complexity quality metrics

Library complexity (filtered non-mito BAM)

	rep1	rep2	ctl1
Total Fragments	7674115	6515021	7441180
Distinct Fragments	6693012	5721282	6570449
Positions with Two Read	788727	645492	717715
NRF = Distinct/Total	0.872154	0.878168	0.882985
PBC1 = OneRead/Distinct	0.868572	0.874912	0.879657
PBC2 = OneRead/TwoRead	7.370562	7.754734	8.052978

Mitochondrial reads are filtered out by default. The non-redundant fraction (NRF) is the fraction of non-redundant mapped reads in a dataset; it is the ratio between the number of positions in the genome that uniquely mapped reads map to and the total number of uniquely mappable reads. The NRF should be > 0.8. The PBC1 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with AT LEAST one read pair. PBC1 is the primary measure, and the PBC1 should be close to 1. Provisionally 0-0.5 is severe bottlenecking, 0.5-0.8 is moderate bottlenecking, 0.8-0.9 is mild bottlenecking, and 0.9-1.0 is no bottlenecking. The PBC2 is the ratio of genomic locations with EXACTLY one read pair over the genomic locations with EXACTLY two read pairs. The PBC2 should be significantly greater than 1. See more details at the ENCODE portal standard for ChIP-Seq pipeline

NRF (non redundant fraction)
PBC1 (PCR Bottleneck coefficient 1)
PBC2 (PCR Bottleneck coefficient 2)
PBC1 is the primary measure. Provisionally

0-0.5 is severe bottlenecking
0.5-0.8 is moderate bottlenecking
0.8-0.9 is mild bottlenecking
0.9-1.0 is no bottlenecking

Replication quality metrics

IDR (Irreproducible Discovery Rate) plots

Reproducibility QC and peak detection statistics

	overlap	idr
Nt	79773	483
N1	40922	156
N2	40314	92
Np	87075	732
N optimal	87075	732
N conservative	79773	483
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0915347297957956	1.515527950310559
Self Consistency Ratio	1.0150816093664732	1.6956521739130435
Reproducibility Test	pass	pass

Reproducibility QC

N1: Replicate 1 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep1 reads)
N2: Replicate 2 self-consistent peaks (comparing two pseudoreplicates generated by subsampling Rep2 reads)
Ni: Replicate i self-consistent peaks (comparing two pseudoreplicates generated by subsampling RepX reads)
Nt: True Replicate consistent peaks (comparing true replicates Rep1 vs Rep2)
Np: Pooled-pseudoreplicate consistent peaks (comparing two pseudoreplicates generated by subsampling pooled reads from Rep1 and Rep2)
Self-consistency Ratio: max(N1,N2) / min (N1,N2)
Rescue Ratio: max(Np,Nt) / min (Np,Nt)
Reproducibility Test: If Self-consistency Ratio >2 AND Rescue Ratio > 2, then 'Fail' else 'Pass'

Number of raw peaks

	rep1	rep2
Number of peaks	142779	131674

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	61.0	210.0	59.0	59.0
25 percentile	230.0	210.0	236.0	236.0
50 percentile (median)	230.0	210.0	236.0	236.0
75 percentile	230.0	210.0	236.0	236.0
Max size	230.0	210.0	236.0	236.0
Mean	229.99580470517373	210.0	234.66120218579235	235.98868791271892

Enrichment / Signal-to-noise ratio

Strand cross-correlation measures (trimmed/filtered SE BAM)

	rep1	rep2
Number of Subsampled Reads	7209810	6116849
Estimated Fragment Length	135	120
Cross-correlation at Estimated Fragment Length	0.690976007012076	0.657388990048431
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6910147	0.6574701
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6864333	0.6532572
NSC (Normalized Strand Cross-correlation coeff.)	1.006618	1.006325
RSC (Relative Strand Cross-correlation coeff.)	0.9915571	0.9807583

Performed on subsampled (15000000) reads mapped from FASTQs that are trimmed to 50. Such FASTQ trimming and subsampling reads are for cross-corrleation analysis only. Untrimmed FASTQs are used for all the other analyses.

NOTE1: For SE datasets, reads from replicates are randomly subsampled to 15000000.
NOTE2: For PE datasets, the first end (R1) of each read-pair is selected and trimmed to 50 the reads are then randomly subsampled to 15000000.

Normalized strand cross-correlation coefficient (NSC) = col9 in outFile
Relative strand cross-correlation coefficient (RSC) = col10 in outFile
Estimated fragment length = col3 in outFile, take the top value

Jensen-Shannon distance (filtered/deduped BAM)

	rep1	rep2
AUC	0.41134794236579897	0.40949893511300606
Synthetic AUC	0.49823760913414766	0.4980819409167847
X-intercept	0.01913036189016358	0.01945369195027902
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5086500770403724	0.505979610247567
Synthetic Elbow Point	0.5029475245313844	0.5023451202434974
JS Distance	0.0367597174244983	0.03814221202398378
Synthetic JS Distance	0.13585101862349333	0.1374702780647506
% Genome Enriched	44.05930911152093	44.715748968138016
Diff. Enrichment	8.930607281502112	9.234691414668173
CHANCE Divergence	0.0759318160958363	0.07856876464839235

Peak enrichment

Fraction of reads in peaks (FRiP)

FRiP for spp raw peaks

	rep1	rep2	rep1-pr1	rep2-pr1	rep1-pr2	rep2-pr2	pooled	pooled-pr1	pooled-pr2
Fraction of Reads in Peaks	0.5339546015251863	0.4847194347861595	0.40575224814640076	0.4214057713393073	0.41136414683334305	0.4196591132217432	0.5288752292628719	0.5344802870368753	0.5352201107765523

FRiP for overlap peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.31217086132365185	0.1798413878790832	0.16951688882170082	0.3358594360521762

FRiP for IDR peaks

	rep1_vs_rep2	rep1-pr1_vs_rep1-pr2	rep2-pr1_vs_rep2-pr2	pooled-pr1_vs_pooled-pr2
Fraction of Reads in Peaks	0.003928001167316609	0.0017303032427736665	0.001003129458087677	0.005470915669223348

For spp raw peaks:

repX: Peak from true replicate X
repX-prY: Peak from Yth pseudoreplicates from replicate X
pooled: Peak from pooled true replicates (pool of rep1, rep2, ...)
pooled-pr1: Peak from 1st pooled pseudo replicate (pool of rep1-pr1, rep2-pr1, ...)
pooled-pr2: Peak from 2nd pooled pseudo replicate (pool of rep1-pr2, rep2-pr2, ...)

For overlap/IDR peaks:

repX_vs_repY: Comparing two peaks from true replicates X and Y
repX-pr1_vs_repX-pr2: Comparing two peaks from both pseudoreplicates from replicate X
pooled-pr1_vs_pooled-pr2: Comparing two peaks from 1st and 2nd pooled pseudo replicates