QC Report

	general
Report generated at	2021-09-12 19:49:22
Title	ceh-91_RW12305_youngadult_1_1
Description	mkudron
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	24035676	12480500	21161810
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	23966831	12448886	21128702
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.8
Paired Reads	24035676	12480500	21161810
Paired Reads (QC-failed)	0	0	0
Read1	12017838	6240250	10580905
Read1 (QC-failed)	0	0	0
Read2	12017838	6240250	10580905
Read2 (QC-failed)	0	0	0
Properly Paired Reads	23855482	12372464	20978970
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.1	99.1
With itself	23945826	12438398	21111494
With itself (QC-failed)	0	0	0
Singletons	21005	10488	17208
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	14332	15885	45578
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10837421	5477274	9597899
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2183980	706976	1600104
Paired Optical Duplicate Reads	203534	56649	160127
% Duplicate Reads	20.1522	12.907399999999999	16.6714

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	17306882	9540596	15995590
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17306882	9540596	15995590
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17306882	9540596	15995590
Paired Reads (QC-failed)	0	0	0
Read1	8653441	4770298	7997795
Read1 (QC-failed)	0	0	0
Read2	8653441	4770298	7997795
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17306882	9540596	15995590
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	17306882	9540596	15995590
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	10794340	5453822	9525824
Distinct Fragments	8628793	4753768	7944958
Positions with Two Read	1469954	555220	1171664
NRF = Distinct/Total	0.799381	0.87164	0.834044
PBC1 = OneRead/Distinct	0.792937	0.868899	0.82857
PBC2 = OneRead/TwoRead	4.654629	7.439476	5.618467

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	33768	1612
N1	27528	1180
N2	28389	974
Np	31966	1716
N optimal	33768	1716
N conservative	33768	1612
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0563723956703999	1.064516129032258
Self Consistency Ratio	1.0312772449869223	1.211498973305955
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	67642	68614

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	75.0	68.0	78.0	78.0
25 percentile	300.0	270.0	310.0	310.0
50 percentile (median)	300.0	270.0	310.0	310.0
75 percentile	300.0	270.0	310.0	310.0
Max size	324.0	284.0	340.0	340.0
Mean	299.4780609680376	269.6361383974116	282.22435897435895	308.60089433783463

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	10138051	5119025
Estimated Fragment Length	180	160
Cross-correlation at Estimated Fragment Length	0.731274966318644	0.613213882070937
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7296282	0.6117761
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.724802	0.6063554
NSC (Normalized Strand Cross-correlation coeff.)	1.008931	1.011311
RSC (Relative Strand Cross-correlation coeff.)	1.341202	1.265239

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	0.41584279044437944	0.40305072468869885
Synthetic AUC	0.49846897988379685	0.49793376180734633
X-intercept	0.018767130671212887	0.01956764331871383
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5257990653366046	0.529480225740574
Synthetic Elbow Point	0.49939009612024343	0.501429523511087
JS Distance	0.04816821707642292	0.0625293635427163
Synthetic JS Distance	0.12958922393286837	0.1435324206200633
% Genome Enriched	42.18082802153599	43.022663890491465
Diff. Enrichment	7.949066926775922	9.946964825940452
CHANCE Divergence	0.06755540826965213	0.08457046600719932

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	0.3403769090238207	0.34500360354845755	0.3381813849333017	0.4009606946987379	0.3401594048147326	0.39307083121431824	0.5288923972672591	0.3309726648460116	0.32305755669545994

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	0.18558279477871253	0.15670534992958293	0.16088187781979238	0.17766052364397134

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	0.019205006891150074	0.015524980178405331	0.01443211723879724	0.019927607352914118

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