QC Report

	general
Report generated at	2023-11-22 17:42:51
Title	zip-7_RW12339_lateembryonic_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	8230024	14995706	12623224
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8205658	14948710	12604064
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.8
Paired Reads	8230024	14995706	12623224
Paired Reads (QC-failed)	0	0	0
Read1	4115012	7497853	6311612
Read1 (QC-failed)	0	0	0
Read2	4115012	7497853	6311612
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8165772	14881624	12494468
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.2	99.0
With itself	8200806	14940370	12596648
With itself (QC-failed)	0	0	0
Singletons	4852	8340	7416
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	9794	15165	52509
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	3703988	6746154	5739758
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	697366	1266678	991343
Paired Optical Duplicate Reads	583093	962219	860828
% Duplicate Reads	18.8274	18.776300000000003	17.2715

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	6013244	10958952	9496830
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	6013244	10958952	9496830
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	6013244	10958952	9496830
Paired Reads (QC-failed)	0	0	0
Read1	3006622	5479476	4748415
Read1 (QC-failed)	0	0	0
Read2	3006622	5479476	4748415
Read2 (QC-failed)	0	0	0
Properly Paired Reads	6013244	10958952	9496830
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	6013244	10958952	9496830
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	3688473	6720626	5707576
Distinct Fragments	3000464	5469834	4732607
Positions with Two Read	424891	790607	628344
NRF = Distinct/Total	0.813471	0.813888	0.82918
PBC1 = OneRead/Distinct	0.82077	0.818952	0.835428
PBC2 = OneRead/TwoRead	5.796054	5.66594	6.292335

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	49882	1190
N1	26958	548
N2	33262	866
Np	49254	1299
N optimal	49882	1299
N conservative	49882	1190
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.012750233483575	1.091596638655462
Self Consistency Ratio	1.2338452407448623	1.5802919708029197
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	66395	111713

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	92.0	91.0	98.0	98.0
25 percentile	370.0	364.0	390.0	390.0
50 percentile (median)	370.0	364.0	390.0	390.0
75 percentile	370.0	364.0	390.0	390.0
Max size	370.0	364.0	390.0	390.0
Mean	369.8951728292793	363.8711967273281	370.6374133949192	389.49015676997715

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	3482785	6339137
Estimated Fragment Length	240	190
Cross-correlation at Estimated Fragment Length	0.48404275777069	0.633010225766603
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.4841266	0.6327667
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.4792026	0.6279058
NSC (Normalized Strand Cross-correlation coeff.)	1.0101	1.008129
RSC (Relative Strand Cross-correlation coeff.)	0.9829635	1.050095

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	0.39508400067346705	0.40563464411656036
Synthetic AUC	0.4974059039128325	0.4980772978755263
X-intercept	0.01954209504192439	0.0187117905237505
Synthetic X-intercept	0.0	0.0
Elbow Point	0.528828132952511	0.5249181172046681
Synthetic Elbow Point	0.5012436786024965	0.5026191847712822
JS Distance	0.05223997776286235	0.03997123800253386
Synthetic JS Distance	0.15053072305782653	0.13914863407660083
% Genome Enriched	42.69381922115041	42.62336309256498
Diff. Enrichment	11.431728181577578	9.706098680594877
CHANCE Divergence	0.09722875245601285	0.0825045229139635

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	0.40407457272646846	0.5455803620638178	0.43276574175270455	0.40683397463553084	0.4331738409417612	0.40809431412784725	0.5392838970278213	0.45169888445785095	0.44635473217490534

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	0.29128110469617485	0.19074911977628048	0.21286871226372742	0.29208895537147933

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	0.015822171744893827	0.009681629416667609	0.012464878028483015	0.016716457905624

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