QC Report

	general
Report generated at	2023-07-21 18:06:49
Title	nfyc-1_RW12333_youngadult_1_2
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	14586180	15516282	13853104
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14328207	15451888	13805159
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.2	99.6	99.7
Paired Reads	14586180	15516282	13853104
Paired Reads (QC-failed)	0	0	0
Read1	7293090	7758141	6926552
Read1 (QC-failed)	0	0	0
Read2	7293090	7758141	6926552
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14272730	15367420	13707484
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.89999999999999	99.0	98.9
With itself	14306742	15425088	13785780
With itself (QC-failed)	0	0	0
Singletons	21465	26800	19379
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.2	0.1
Diff. Chroms	5979	11825	32607
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6521433	7043250	6263363
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1204901	810968	895506
Paired Optical Duplicate Reads	71338	53698	56579
% Duplicate Reads	18.476	11.5141	14.2975

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	10633064	12464564	10735714
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10633064	12464564	10735714
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10633064	12464564	10735714
Paired Reads (QC-failed)	0	0	0
Read1	5316532	6232282	5367857
Read1 (QC-failed)	0	0	0
Read2	5316532	6232282	5367857
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10633064	12464564	10735714
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10633064	12464564	10735714
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	6479609	6993162	6190295
Distinct Fragments	5293173	6194340	5314957
Positions with Two Read	843935	657092	676015
NRF = Distinct/Total	0.816897	0.885771	0.858595
PBC1 = OneRead/Distinct	0.810775	0.883036	0.85517
PBC2 = OneRead/TwoRead	5.085193	8.324288	6.723506

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	76607	1397
N1	32447	617
N2	33245	658
Np	77661	1447
N optimal	77661	1447
N conservative	76607	1397
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0137585338154478	1.0357909806728705
Self Consistency Ratio	1.0245939532160138	1.0664505672609401
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	119086	121156

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	74.0	81.0	84.0	84.0
25 percentile	296.0	324.0	336.0	336.0
50 percentile (median)	296.0	324.0	336.0	336.0
75 percentile	296.0	324.0	336.0	336.0
Max size	530.0	561.0	582.0	582.0
Mean	295.9526812555632	323.9532173396282	327.78852798894263	335.84396286424334

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6066225	6606127
Estimated Fragment Length	190	205
Cross-correlation at Estimated Fragment Length	0.629088020054088	0.676455394189765
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6284203	0.6757481
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6240962	0.6717518
NSC (Normalized Strand Cross-correlation coeff.)	1.007998	1.007002
RSC (Relative Strand Cross-correlation coeff.)	1.154426	1.176978

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	0.40688958963254274	0.41104562629358593
Synthetic AUC	0.49804578128906396	0.4981964814982411
X-intercept	0.019298637837147282	0.018911387553696046
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5302194950575686	0.5275466696475624
Synthetic Elbow Point	0.5022667647413332	0.49989664720347127
JS Distance	0.04564044308520544	0.040138152045981056
Synthetic JS Distance	0.14144092770138258	0.13807579117317895
% Genome Enriched	43.289192124047844	43.60178694048322
Diff. Enrichment	9.709354076512527	9.005063768902488
CHANCE Divergence	0.08254083697442108	0.07654619229230605

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	0.5324573424931892	0.5482332153776097	0.40703206526359664	0.3975413821133254	0.39800531624750873	0.3994138904497582	0.5422462860688552	0.5471383468466978	0.5487442260304825

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	0.3786587956131253	0.18221314195042934	0.1927700800445166	0.3828435976196344

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	0.016042642993471017	0.009294404698401138	0.009469725535526153	0.016534078737435724

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