QC Report

	general
Report generated at	2021-08-28 14:52:15
Title	ceh-100_RW12233_youngadult_1_4
Description	gevirl
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	19294736	18917672	20768690
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19075251	18739468	20687049
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.9	99.1	99.6
Paired Reads	19294736	18917672	20768690
Paired Reads (QC-failed)	0	0	0
Read1	9647368	9458836	10384345
Read1 (QC-failed)	0	0	0
Read2	9647368	9458836	10384345
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19045888	18670938	20611540
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.7	98.7	99.2
With itself	19067692	18730422	20677484
With itself (QC-failed)	0	0	0
Singletons	7559	9046	9565
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	4044	4082	28727
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8689913	8539978	9480500
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1123485	1173205	872045
Paired Optical Duplicate Reads	61606	57913	61659
% Duplicate Reads	12.928600000000001	13.7378	9.1983

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	15132856	14733546	17216910
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15132856	14733546	17216910
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	15132856	14733546	17216910
Paired Reads (QC-failed)	0	0	0
Read1	7566428	7366773	8608455
Read1 (QC-failed)	0	0	0
Read2	7566428	7366773	8608455
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15132856	14733546	17216910
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	15132856	14733546	17216910
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	8586392	8384437	9379466
Distinct Fragments	7486883	7258661	8523132
Positions with Two Read	876088	881916	745980
NRF = Distinct/Total	0.871947	0.86573	0.908701
PBC1 = OneRead/Distinct	0.868933	0.862758	0.906269
PBC2 = OneRead/TwoRead	7.425737	7.100981	10.354503

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	13324	1707
N1	20113	1182
N2	14564	1360
Np	14168	1911
N optimal	14168	1911
N conservative	13324	1707
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.063344341038727	1.1195079086115993
Self Consistency Ratio	1.3810079648448228	1.1505922165820643
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	42604	25780

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	79.0	66.0	79.0	79.0
25 percentile	316.0	264.0	311.0	316.0
50 percentile (median)	316.0	264.0	316.0	316.0
75 percentile	316.0	264.0	316.0	316.0
Max size	844.0	1431.0	1132.0	1132.0
Mean	315.1825415453948	263.06408068269974	289.5651491365777	312.2876199887069

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8065613	7894159
Estimated Fragment Length	150	140
Cross-correlation at Estimated Fragment Length	0.715403666243778	0.710819460301605
Phantom Peak	55	50
Cross-correlation at Phantom Peak	0.7127189	0.7078123
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7043466	0.6988323
NSC (Normalized Strand Cross-correlation coeff.)	1.015698	1.017153
RSC (Relative Strand Cross-correlation coeff.)	1.320671	1.334879

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	0.388720725856394	0.390422760180341
Synthetic AUC	0.49835281488562316	0.4983200389382427
X-intercept	0.01912598310428343	0.019503351389773518
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5523174206378523	0.5821414951371404
Synthetic Elbow Point	0.5013089166647472	0.5028136418176979
JS Distance	0.06618480665663236	0.0751489074756204
Synthetic JS Distance	0.1766027340686307	0.1809954152098413
% Genome Enriched	34.54756737221891	30.74593131098541
Diff. Enrichment	8.17974498353422	8.722079456766618
CHANCE Divergence	0.06988603152601533	0.07556782136975512

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	0.259860795609236	0.16727324162153495	0.31938716657318356	0.27108351633971667	0.3201284674882256	0.27906904136574334	0.4865134072728278	0.20558189730507898	0.20510808132215466

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	0.1061525255034068	0.14353371234088264	0.11267776270559715	0.11252711324249905

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	0.0373357661227489	0.028709187479217406	0.03888133922410803	0.03986559880898945

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