QC Report

	general
Report generated at	2021-08-29 15:34:27
Title	egrh-3_RW12196_youngadult_1_7
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	58134728	42415104	55822424
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	40703992	27046752	45653419
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	70.0	63.800000000000004	81.8
Paired Reads	58134728	42415104	55822424
Paired Reads (QC-failed)	0	0	0
Read1	29067364	21207552	27911212
Read1 (QC-failed)	0	0	0
Read2	29067364	21207552	27911212
Read2 (QC-failed)	0	0	0
Properly Paired Reads	39149712	26256558	45353602
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	67.30000000000001	61.9	81.2
With itself	40402914	26880234	45604952
With itself (QC-failed)	0	0	0
Singletons	301078	166518	48467
Singletons (QC-failed)	0	0	0
% Singleton	0.5	0.4	0.1
Diff. Chroms	272266	135580	111300
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	15742224	10904071	20614316
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	11868983	6340592	2863805
Paired Optical Duplicate Reads	92685	57412	118450
% Duplicate Reads	75.39580000000001	58.148900000000005	13.892299999999999

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	7746482	9126958	35501022
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	7746482	9126958	35501022
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	7746482	9126958	35501022
Paired Reads (QC-failed)	0	0	0
Read1	3873241	4563479	17750511
Read1 (QC-failed)	0	0	0
Read2	3873241	4563479	17750511
Read2 (QC-failed)	0	0	0
Properly Paired Reads	7746482	9126958	35501022
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	7746482	9126958	35501022
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	15628989	10801846	20481348
Distinct Fragments	4048675	4715229	17653391
Positions with Two Read	692732	1247309	1869207
NRF = Distinct/Total	0.259049	0.436521	0.861925
PBC1 = OneRead/Distinct	0.224272	0.414579	0.880977
PBC2 = OneRead/TwoRead	1.310761	1.567244	8.320232

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	19955	2218
N1	19432	2868
N2	18775	1463
Np	20101	3278
N optimal	20101	3278
N conservative	19955	2218
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0073164620395891	1.477908025247971
Self Consistency Ratio	1.034993342210386	1.9603554340396445
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	41816	42854

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	105.0	94.0	100.0	100.0
25 percentile	420.0	376.0	259.0	400.0
50 percentile (median)	420.0	376.0	400.0	400.0
75 percentile	420.0	376.0	400.0	400.0
Max size	2114.0	1317.0	2095.0	2095.0
Mean	416.61428639755115	374.8243571195221	358.34014643075045	392.62449629371673

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	13686706	9665347
Estimated Fragment Length	210	205
Cross-correlation at Estimated Fragment Length	0.597418800338031	0.615799312466164
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.5648287	0.6045418
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5481854	0.5975929
NSC (Normalized Strand Cross-correlation coeff.)	1.089812	1.030466
RSC (Relative Strand Cross-correlation coeff.)	2.958145	2.620036

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	0.34324464339774163	0.37507630551936644
Synthetic AUC	0.4980025124311305	0.4981768916692956
X-intercept	0.017963150564770245	0.01782328176170752
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6437381735931696	0.5916570257098841
Synthetic Elbow Point	0.5015978223014005	0.4993583903846078
JS Distance	0.16631981359984793	0.0996058483665642
Synthetic JS Distance	0.24473040242360164	0.1906331672077953
% Genome Enriched	29.344275069984356	34.68866203501116
Diff. Enrichment	16.376619600909496	11.586300731673106
CHANCE Divergence	0.14116756758543972	0.0988942507252598

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	0.35712094858027166	0.31665775168462484	0.39428597541800897	0.36797707013068975	0.39189231754293563	0.36488814014223364	0.3194394859613689	0.33251682347717515	0.32932770776503373

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	0.1952550280203681	0.22491061103608065	0.17335622668582457	0.19839985207521407

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	0.05789874500990906	0.0867606740711461	0.036364142357179684	0.07116391204164652

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