QC Report

	general
Report generated at	2021-09-01 15:06:24
Title	zfp-3_RW12271_L4larva_1_3
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	15655194	14406998	12300022
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15606486	14358972	12238642
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.5
Paired Reads	15655194	14406998	12300022
Paired Reads (QC-failed)	0	0	0
Read1	7827597	7203499	6150011
Read1 (QC-failed)	0	0	0
Read2	7827597	7203499	6150011
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15560266	14314312	12158210
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.4	98.8
With itself	15594964	14347596	12230336
With itself (QC-failed)	0	0	0
Singletons	11522	11376	8306
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5097	4150	5249
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7173777	6593156	5586175
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1199580	994747	785917
Paired Optical Duplicate Reads	72192	59147	49169
% Duplicate Reads	16.721700000000002	15.087600000000002	14.069

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	11948394	11196818	9600516
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11948394	11196818	9600516
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11948394	11196818	9600516
Paired Reads (QC-failed)	0	0	0
Read1	5974197	5598409	4800258
Read1 (QC-failed)	0	0	0
Read2	5974197	5598409	4800258
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11948394	11196818	9600516
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11948394	11196818	9600516
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	7122720	6544770	5508183
Distinct Fragments	5938145	5565711	4737873
Positions with Two Read	870318	743155	600945
NRF = Distinct/Total	0.833691	0.850406	0.860152
PBC1 = OneRead/Distinct	0.828869	0.846662	0.856353
PBC2 = OneRead/TwoRead	5.655337	6.340909	6.751521

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	80231	2010
N1	27544	931
N2	29128	933
Np	34359	1458
N optimal	80231	2010
N conservative	80231	2010
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	2.335079600686865	1.3786008230452675
Self Consistency Ratio	1.0575079872204474	1.0021482277121374
Reproducibility Test	borderline	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	125440	126261

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	72.0	69.0	84.0	84.0
25 percentile	290.0	276.0	336.0	336.0
50 percentile (median)	290.0	276.0	336.0	336.0
75 percentile	290.0	276.0	336.0	336.0
Max size	1340.0	1362.0	1760.0	1760.0
Mean	289.9294882015306	275.9336612255566	327.70248756218905	335.787949794967

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6707559	6165496
Estimated Fragment Length	155	145
Cross-correlation at Estimated Fragment Length	0.659939714311578	0.648159935321675
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6600675	0.6483127
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6536321	0.641559
NSC (Normalized Strand Cross-correlation coeff.)	1.00965	1.010289
RSC (Relative Strand Cross-correlation coeff.)	0.980149	0.9773775

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	0.39881749571506264	0.39559760082763856
Synthetic AUC	0.4981571008359982	0.49809149955833576
X-intercept	0.01932879101755058	0.019588237876846562
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5756147892692779	0.5776863726535028
Synthetic Elbow Point	0.5029068596053508	0.501804177228052
JS Distance	0.06912478957293278	0.07119409898659664
Synthetic JS Distance	0.15828106973026898	0.16208426480932794
% Genome Enriched	38.56677563434757	37.8347363421186
Diff. Enrichment	9.26529973504316	9.690243660033948
CHANCE Divergence	0.07887327637945994	0.08254681014565386

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	0.5411088720375308	0.5363965905313456	0.3579168283341128	0.3654255404659537	0.34264242418561425	0.3538182640493512	0.5330537045847754	0.5362847337436817	0.23196335068580934

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	0.3951151538382971	0.1618153033788474	0.16663975425875457	0.20126931652213859

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	0.02678126257819544	0.014824251694411818	0.014921292817298629	0.021003436909543104

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