QC Report

	general
Report generated at	2021-11-05 00:49:22
Title	pie-1_RW12313_earlyembryonic_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	16077958	15298640	15826090
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15859495	15262921	15804843
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.6	99.8	99.9
Paired Reads	16077958	15298640	15826090
Paired Reads (QC-failed)	0	0	0
Read1	8038979	7649320	7913045
Read1 (QC-failed)	0	0	0
Read2	8038979	7649320	7913045
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15773278	15162732	15721700
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.1	99.1	99.3
With itself	15847352	15253520	15791908
With itself (QC-failed)	0	0	0
Singletons	12143	9401	12935
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	7125	5548	9312
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7068215	6802859	7223844
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	895543	782941	741730
Paired Optical Duplicate Reads	85753	68236	75943
% Duplicate Reads	12.67	11.509	10.267800000000001

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	12345344	12039836	12964228
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12345344	12039836	12964228
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12345344	12039836	12964228
Paired Reads (QC-failed)	0	0	0
Read1	6172672	6019918	6482114
Read1 (QC-failed)	0	0	0
Read2	6172672	6019918	6482114
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12345344	12039836	12964228
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12345344	12039836	12964228
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	7042936	6776848	7187868
Distinct Fragments	6153078	5999438	6451606
Positions with Two Read	723797	642908	628625
NRF = Distinct/Total	0.873652	0.885284	0.897569
PBC1 = OneRead/Distinct	0.86967	0.882242	0.894563
PBC2 = OneRead/TwoRead	7.393161	8.232837	9.180938

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	82294	1005
N1	32617	438
N2	31267	463
Np	82269	1004
N optimal	82294	1005
N conservative	82294	1005
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.000303881170307	1.000996015936255
Self Consistency Ratio	1.0431765119774843	1.0570776255707763
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	134661	136220

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	66.0	64.0	70.0	70.0
25 percentile	264.0	256.0	280.0	280.0
50 percentile (median)	264.0	256.0	280.0	280.0
75 percentile	264.0	256.0	280.0	280.0
Max size	264.0	256.0	280.0	280.0
Mean	263.95247324763665	255.9599324621935	268.57114427860694	279.8595887914064

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6619674	6383030
Estimated Fragment Length	170	165
Cross-correlation at Estimated Fragment Length	0.673383970241752	0.670560522786076
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6740833	0.6708802
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6697785	0.6665002
NSC (Normalized Strand Cross-correlation coeff.)	1.005383	1.006092
RSC (Relative Strand Cross-correlation coeff.)	0.8375362	0.9270172

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	0.4161879928127848	0.41543875012127196
Synthetic AUC	0.49817895561791625	0.4981574155171559
X-intercept	0.018923288819689802	0.018921292692177176
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5057987504241771	0.5070203804619039
Synthetic Elbow Point	0.500249565757584	0.5000723100523945
JS Distance	0.027671403900655287	0.02804090651412583
Synthetic JS Distance	0.12470045248445856	0.1259867150071527
% Genome Enriched	43.82557837794678	42.94029582609737
Diff. Enrichment	8.081409862080086	8.166385378254814
CHANCE Divergence	0.06868825408076872	0.06939778167503668

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	0.5413606943638023	0.5407478972304939	0.39114001197536497	0.3828028886772212	0.3806000059617618	0.3682467103372504	0.5366853966220466	0.5405805493336526	0.5409499540294556

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	0.35212399498383856	0.15963054573448904	0.15224368504687272	0.3519271541157375

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	0.009605219235617699	0.005295599701393497	0.00554251735654871	0.009650000533110685

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