QC Report

	general
Report generated at	2023-08-15 11:05:33
Title	madf-1_RW12345_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	10456952	11377666	10864050
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10413949	11319122	10838236
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.5	99.8
Paired Reads	10456952	11377666	10864050
Paired Reads (QC-failed)	0	0	0
Read1	5228476	5688833	5432025
Read1 (QC-failed)	0	0	0
Read2	5228476	5688833	5432025
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10323438	11242320	10714626
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.7	98.8	98.6
With itself	10400128	11308522	10825064
With itself (QC-failed)	0	0	0
Singletons	13821	10600	13172
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	14108	12052	56808
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4555932	5062620	4884824
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	495503	520133	609379
Paired Optical Duplicate Reads	32311	32887	49672
% Duplicate Reads	10.876	10.274	12.4749

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	8120858	9084974	8550890
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8120858	9084974	8550890
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8120858	9084974	8550890
Paired Reads (QC-failed)	0	0	0
Read1	4060429	4542487	4275445
Read1 (QC-failed)	0	0	0
Read2	4060429	4542487	4275445
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8120858	9084974	8550890
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8120858	9084974	8550890
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	4524669	5028415	4834164
Distinct Fragments	4035932	4515118	4236173
Positions with Two Read	406553	430005	488291
NRF = Distinct/Total	0.891984	0.897921	0.876299
PBC1 = OneRead/Distinct	0.889591	0.895977	0.872392
PBC2 = OneRead/TwoRead	8.831141	9.407893	7.568448

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	31428	1044
N1	25646	514
N2	27234	472
Np	26364	1014
N optimal	31428	1044
N conservative	31428	1044
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1920801092398725	1.029585798816568
Self Consistency Ratio	1.0619199875224206	1.0889830508474576
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	62261	69387

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	79.0	81.0	81.0
25 percentile	300.0	300.0	310.0	310.0
50 percentile (median)	300.0	300.0	310.0	310.0
75 percentile	300.0	300.0	310.0	310.0
Max size	300.0	300.0	310.0	310.0
Mean	299.92497711247813	299.9459841180625	303.4990421455939	309.784046073565

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4261541	4741017
Estimated Fragment Length	185	195
Cross-correlation at Estimated Fragment Length	0.57734950702958	0.605184267731299
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5767876	0.6039114
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5724265	0.6003919
NSC (Normalized Strand Cross-correlation coeff.)	1.0086	1.007982
RSC (Relative Strand Cross-correlation coeff.)	1.128832	1.361668

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	0.4036962849296949	0.407832883447046
Synthetic AUC	0.4977628706435461	0.49788684593394783
X-intercept	0.019396611928088274	0.019173134864417265
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5312907795757926	0.5253726280503621
Synthetic Elbow Point	0.5023532308681141	0.5036839325636379
JS Distance	0.040579235960679576	0.0351649502879037
Synthetic JS Distance	0.14373819005367225	0.1387181909621546
% Genome Enriched	42.73559869904424	43.90645888620628
Diff. Enrichment	10.397732894137784	9.758053550100826
CHANCE Divergence	0.08839325276689573	0.08297371917743698

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	0.3309974143126256	0.35577515136532034	0.3833379715941415	0.3789575228377048	0.3841585172794592	0.3843010193096908	0.5534346144958291	0.3133521672530181	0.30149423788265234

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	0.1720478265741523	0.1528815058704388	0.15706891401120135	0.1484314737003128

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	0.012016506961128064	0.007572598855933695	0.006644708064106733	0.011645934936479677

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