QC Report

	general
Report generated at	2021-08-28 14:08:38
Title	ceh-45_RW12292_lateembryonic_1_2
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	12644224	13128336	11489336
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12614521	13058633	11468098
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	99.5	99.8
Paired Reads	12644224	13128336	11489336
Paired Reads (QC-failed)	0	0	0
Read1	6322112	6564168	5744668
Read1 (QC-failed)	0	0	0
Read2	6322112	6564168	5744668
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12545988	12971150	11333182
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	98.8	98.6
With itself	12606668	13049838	11458398
With itself (QC-failed)	0	0	0
Singletons	7853	8795	9700
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6515	6990	7678
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5612954	5803435	5189177
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	824900	1135693	846739
Paired Optical Duplicate Reads	40238	57627	46895
% Duplicate Reads	14.6964	19.569300000000002	16.317400000000003

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	9576108	9335484	8684876
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9576108	9335484	8684876
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9576108	9335484	8684876
Paired Reads (QC-failed)	0	0	0
Read1	4788054	4667742	4342438
Read1 (QC-failed)	0	0	0
Read2	4788054	4667742	4342438
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9576108	9335484	8684876
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9576108	9335484	8684876
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	5594995	5785819	5166179
Distinct Fragments	4773443	4654705	4324200
Positions with Two Read	634051	794163	632297
NRF = Distinct/Total	0.853163	0.804502	0.837021
PBC1 = OneRead/Distinct	0.848831	0.796215	0.831158
PBC2 = OneRead/TwoRead	6.390409	4.666731	5.684185

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	46265	463
N1	30390	258
N2	30978	227
Np	77625	548
N optimal	77625	548
N conservative	46265	463
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.6778342159299686	1.183585313174946
Self Consistency Ratio	1.0193484698914117	1.1365638766519823
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	78120	93409

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	101.0	95.0	76.0	76.0
25 percentile	300.0	276.0	304.0	304.0
50 percentile (median)	300.0	276.0	304.0	304.0
75 percentile	300.0	276.0	304.0	304.0
Max size	300.0	276.0	304.0	304.0
Mean	299.98858166922685	275.99208855677716	299.54379562043795	303.9665185185185

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5270738	5459117
Estimated Fragment Length	190	170
Cross-correlation at Estimated Fragment Length	0.610853555465971	0.597029688646829
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6115257	0.5976886
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6073738	0.5935309
NSC (Normalized Strand Cross-correlation coeff.)	1.005729	1.005895
RSC (Relative Strand Cross-correlation coeff.)	0.8381098	0.8415213

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	0.4102116264953807	0.40989127106043516
Synthetic AUC	0.4979399161215049	0.4979098142256689
X-intercept	0.019376503968681534	0.019540119798712622
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5100923032719176	0.5066563708412647
Synthetic Elbow Point	0.5032039112701043	0.4985775609114051
JS Distance	0.02371434804545993	0.02407444128695885
Synthetic JS Distance	0.13014274452718738	0.13014092694965584
% Genome Enriched	44.01984141236377	43.88435952383803
Diff. Enrichment	8.64652135455099	8.673890540695982
CHANCE Divergence	0.07353219916722475	0.07375990668933628

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	0.38845530981897863	0.4300531177601504	0.39072178383953066	0.3923783705269057	0.39205948805088664	0.39090892341521877	0.5746405167793383	0.5572539847517861	0.5315425586592604

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	0.23067518588598993	0.16806880206447128	0.16172509106115976	0.3591656376681561

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	0.005217011872929576	0.0035713882926132414	0.0031154249742166556	0.0058559321711255195

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