QC Report

	general
Report generated at	2021-09-14 00:59:20
Title	hmg-1.2_RW12210_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	17015646	19901246	14640410
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16869257	19843817	14389558
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.1	99.7	98.3
Paired Reads	17015646	19901246	14640410
Paired Reads (QC-failed)	0	0	0
Read1	8507823	9950623	7320205
Read1 (QC-failed)	0	0	0
Read2	8507823	9950623	7320205
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16809034	19760960	14330752
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.8	99.3	97.89999999999999
With itself	16858796	19820466	14381184
With itself (QC-failed)	0	0	0
Singletons	10461	23351	8374
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6200	15375	10686
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7679527	8955056	6561133
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1545007	1044282	1230863
Paired Optical Duplicate Reads	75091	105846	66113
% Duplicate Reads	20.1185	11.6614	18.7599

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	12269040	15821548	10660540
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12269040	15821548	10660540
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12269040	15821548	10660540
Paired Reads (QC-failed)	0	0	0
Read1	6134520	7910774	5330270
Read1 (QC-failed)	0	0	0
Read2	6134520	7910774	5330270
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12269040	15821548	10660540
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12269040	15821548	10660540
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	7638016	8925060	6489523
Distinct Fragments	6103656	7890723	5274533
Positions with Two Read	1055182	852106	869777
NRF = Distinct/Total	0.799115	0.884109	0.812777
PBC1 = OneRead/Distinct	0.791222	0.881083	0.80486
PBC2 = OneRead/TwoRead	4.57679	8.159059	4.880859

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	35426	4149
N1	24647	3340
N2	21962	5333
Np	41270	6058
N optimal	41270	6058
N conservative	35426	4149
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1649635860667307	1.460110870089178
Self Consistency Ratio	1.122256625079683	1.5967065868263473
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	89244	49916

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	80.0	79.0	82.0	82.0
25 percentile	320.0	316.0	236.0	330.0
50 percentile (median)	320.0	316.0	330.0	330.0
75 percentile	320.0	316.0	330.0	330.0
Max size	807.0	1124.0	1115.0	1115.0
Mean	318.3797902379992	310.585744050004	285.156652360515	323.37482432759873

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7203331	8395512
Estimated Fragment Length	170	165
Cross-correlation at Estimated Fragment Length	0.663000864518236	0.72879853570621
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.6481987	0.7013216
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6341371	0.6761117
NSC (Normalized Strand Cross-correlation coeff.)	1.045517	1.077926
RSC (Relative Strand Cross-correlation coeff.)	2.052664	2.089926

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	0.3717921380276924	0.3622279804647417
Synthetic AUC	0.49817630165254023	0.4983930658248072
X-intercept	0.019477020349185314	0.019373238705763074
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6452204561602388	0.687024500451051
Synthetic Elbow Point	0.4986870124558532	0.5008234508507025
JS Distance	0.13068200822778284	0.16083311201645703
Synthetic JS Distance	0.20468594545577437	0.22746139820145742
% Genome Enriched	31.249051994603356	27.03990803349752
Diff. Enrichment	14.196482034622049	15.604014524477716
CHANCE Divergence	0.12277006059705775	0.13728257980706596

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	0.46331432614124657	0.34162188175265784	0.35464339508225584	0.3316431489510382	0.35769970592646205	0.3336195674405564	0.4370058042216845	0.45962676181787293	0.35986466356631625

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	0.2591530301893289	0.20284333574591004	0.21648437940459428	0.2874283372067541

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	0.09173492559144722	0.07058213193534295	0.11958798216204887	0.10977879850717258

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