QC Report

	general
Report generated at	2021-08-30 13:19:52
Title	flt-1_OP797_earlyembryonic_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}, 'ctl2': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	18410248	11755784	20084932	14378898
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	17663278	11474276	20043472	14345443
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	95.89999999999999	97.6	99.8	99.8
Paired Reads	18410248	11755784	20084932	14378898
Paired Reads (QC-failed)	0	0	0	0
Read1	9205124	5877892	10042466	7189449
Read1 (QC-failed)	0	0	0	0
Read2	9205124	5877892	10042466	7189449
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	16607610	11237920	19637414	14216510
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	90.2	95.6	97.8	98.9
With itself	17624480	11457668	20029936	14334672
With itself (QC-failed)	0	0	0	0
Singletons	38798	16608	13536	10771
Singletons (QC-failed)	0	0	0	0
% Singleton	0.2	0.1	0.1	0.1
Diff. Chroms	18717	5442	81051	32245
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	7469134	5053828	8993872	6483178
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	1069051	896512	1074443	1042620
Paired Optical Duplicate Reads	65969	55523	86270	69610
% Duplicate Reads	14.3129	17.7393	11.9464	16.081899999999997

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	ctl2
Total Reads	12800166	8314632	15838858	10881116
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	12800166	8314632	15838858	10881116
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	12800166	8314632	15838858	10881116
Paired Reads (QC-failed)	0	0	0	0
Read1	6400083	4157316	7919429	5440558
Read1 (QC-failed)	0	0	0	0
Read2	6400083	4157316	7919429	5440558
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	12800166	8314632	15838858	10881116
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	12800166	8314632	15838858	10881116
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl2
Total Fragments	7420447	5004235	8897160	6439871
Distinct Fragments	6386509	4125263	7838453	5406223
Positions with Two Read	801518	641948	873165	780037
NRF = Distinct/Total	0.860664	0.824354	0.881006	0.839492
PBC1 = OneRead/Distinct	0.85753	0.81779	0.877365	0.833781
PBC2 = OneRead/TwoRead	6.83281	5.25525	7.876155	5.778708

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	31867	977
N1	35021	618
N2	27742	767
Np	33223	1083
N optimal	33223	1083
N conservative	31867	977
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0425518561521323	1.1084953940634596
Self Consistency Ratio	1.2623819479489582	1.2411003236245954
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	89892	77764

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	50.0	56.0	58.0	58.0
25 percentile	196.0	224.0	230.0	230.0
50 percentile (median)	196.0	224.0	230.0	230.0
75 percentile	196.0	224.0	230.0	230.0
Max size	230.0	389.0	412.0	412.0
Mean	195.88624126729854	223.81353839823055	211.140350877193	229.39039219817596

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7363617	4788605
Estimated Fragment Length	110	105
Cross-correlation at Estimated Fragment Length	0.693446148522014	0.57761483778083
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.693598	0.5781882
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6877335	0.5718071
NSC (Normalized Strand Cross-correlation coeff.)	1.008306	1.010157
RSC (Relative Strand Cross-correlation coeff.)	0.9741063	0.9101396

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	0.4055379709620989	0.39327623885284513
Synthetic AUC	0.4981339887313045	0.4977350270476286
X-intercept	0.01963700388468126	0.02004423665813607
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5288077262437567	0.5503471459769794
Synthetic Elbow Point	0.4999443344814732	0.5039718782149929
JS Distance	0.049523288476149833	0.06383888910293761
Synthetic JS Distance	0.144797784588893	0.1630122393590852
% Genome Enriched	42.66302286492249	41.064035357386686
Diff. Enrichment	9.028570259919377	10.696354363435223
CHANCE Divergence	0.0767421912025557	0.09093346917663084

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	0.33965926691888215	0.35103321469909915	0.3997160037274511	0.42004095911881606	0.40011846723213856	0.42011047512385397	0.46566389126715774	0.335801238941406	0.3416987784300639

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	0.1450360074484255	0.1471068422081401	0.14666710444912054	0.1508963524064971

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	0.011246804255479971	0.007498496503873465	0.015173972822850127	0.012033977308236622

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