QC Report

	general
Report generated at	2023-04-20 15:39:04
Title	crh-1_RW12338_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	16262088	13798412	13657206
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15365055	13623974	13141356
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	94.5	98.7	96.2
Paired Reads	16262088	13798412	13657206
Paired Reads (QC-failed)	0	0	0
Read1	8131044	6899206	6828603
Read1 (QC-failed)	0	0	0
Read2	8131044	6899206	6828603
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15097600	13377880	12892060
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	92.80000000000001	97.0	94.39999999999999
With itself	15352852	13612494	13125552
With itself (QC-failed)	0	0	0
Singletons	12203	11480	15804
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	27165	20204	143081
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6596722	5959157	5783698
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1130921	979081	822043
Paired Optical Duplicate Reads	76042	59605	58327
% Duplicate Reads	17.1437	16.4299	14.2131

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	10931602	9960152	9923310
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10931602	9960152	9923310
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10931602	9960152	9923310
Paired Reads (QC-failed)	0	0	0
Read1	5465801	4980076	4961655
Read1 (QC-failed)	0	0	0
Read2	5465801	4980076	4961655
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10931602	9960152	9923310
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10931602	9960152	9923310
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	6570628	5937340	5730936
Distinct Fragments	5446297	4965225	4920135
Positions with Two Read	831683	727716	644599
NRF = Distinct/Total	0.828885	0.836271	0.858522
PBC1 = OneRead/Distinct	0.822403	0.83055	0.853058
PBC2 = OneRead/TwoRead	5.385529	5.666863	6.511276

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	20930	3936
N1	19592	2394
N2	19901	4235
Np	21667	4791
N optimal	21667	4791
N conservative	20930	3936
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0352126134734831	1.2172256097560976
Self Consistency Ratio	1.0157717435688036	1.7690058479532165
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	38842	36074

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	99.0	111.0	112.0	112.0
25 percentile	396.0	444.0	412.0	450.0
50 percentile (median)	396.0	444.0	450.0	450.0
75 percentile	396.0	444.0	450.0	450.0
Max size	785.0	1076.0	2304.0	2304.0
Mean	393.7839709592709	436.63877030548315	405.1189730745147	439.2430885678682

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6257117	5690238
Estimated Fragment Length	180	185
Cross-correlation at Estimated Fragment Length	0.640119670684137	0.626552936903281
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6350859	0.6163577
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6272509	0.5998274
NSC (Normalized Strand Cross-correlation coeff.)	1.020516	1.044555
RSC (Relative Strand Cross-correlation coeff.)	1.64246	1.616757

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	0.38096588994658653	0.35242258892430095
Synthetic AUC	0.4980673846521006	0.4979780909625829
X-intercept	0.018697110011176753	0.01900047900367236
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6173598914258343	0.6795325722497206
Synthetic Elbow Point	0.5026328855577009	0.5010749189978181
JS Distance	0.09893049314480523	0.14891891449935013
Synthetic JS Distance	0.18315654489778338	0.2281634515769088
% Genome Enriched	32.573646814625576	27.304806003512695
Diff. Enrichment	12.659713329647593	17.19441920180419
CHANCE Divergence	0.10911693323484829	0.15048736756877948

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	0.28551441956997703	0.3194429161322036	0.32771512762445476	0.34429755690475405	0.3313535072633466	0.34325279373246514	0.3054465412525918	0.3013511166797085	0.3012331373644489

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	0.20543176987437245	0.17680363774678223	0.22756871581879473	0.2112582792234678

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	0.07433574031170384	0.044269632209441946	0.09290209627322957	0.08533462532633689

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