QC Report

	general
Report generated at	2021-09-01 18:23:07
Title	ztf-28_RW12281_youngadult_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	18113982	20031972	21395906
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18086635	19993749	21368868
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	99.8	99.9
Paired Reads	18113982	20031972	21395906
Paired Reads (QC-failed)	0	0	0
Read1	9056991	10015986	10697953
Read1 (QC-failed)	0	0	0
Read2	9056991	10015986	10697953
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18005418	19902634	21213586
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.4	99.1
With itself	18075166	19978672	21353298
With itself (QC-failed)	0	0	0
Singletons	11469	15077	15570
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	16282	15379	43061
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8187100	9024196	9624753
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1051101	1221249	1166816
Paired Optical Duplicate Reads	100062	121324	121581
% Duplicate Reads	12.8385	13.533100000000001	12.1231

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	14271998	15605894	16915874
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14271998	15605894	16915874
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14271998	15605894	16915874
Paired Reads (QC-failed)	0	0	0
Read1	7135999	7802947	8457937
Read1 (QC-failed)	0	0	0
Read2	7135999	7802947	8457937
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14271998	15605894	16915874
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14271998	15605894	16915874
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	8159219	8993896	9558203
Distinct Fragments	7114614	7780605	8403736
Positions with Two Read	842533	968156	952429
NRF = Distinct/Total	0.871972	0.865098	0.879217
PBC1 = OneRead/Distinct	0.868149	0.860718	0.875255
PBC2 = OneRead/TwoRead	7.330926	6.917173	7.722789

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	76946	1086
N1	41817	342
N2	41655	411
Np	77105	1137
N optimal	77105	1137
N conservative	76946	1086
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0020663842175033	1.0469613259668509
Self Consistency Ratio	1.0038890889449046	1.2017543859649122
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	122079	126564

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	71.0	71.0	77.0	77.0
25 percentile	284.0	280.0	300.0	300.0
50 percentile (median)	284.0	280.0	300.0	300.0
75 percentile	284.0	280.0	300.0	300.0
Max size	284.0	280.0	300.0	300.0
Mean	283.96025524455473	279.9658670712051	294.01759014951625	299.9086959341158

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7671674	8459188
Estimated Fragment Length	170	180
Cross-correlation at Estimated Fragment Length	0.703226893711496	0.719735850698124
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7029587	0.7194353
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6985039	0.7152729
NSC (Normalized Strand Cross-correlation coeff.)	1.006762	1.006239
RSC (Relative Strand Cross-correlation coeff.)	1.060213	1.072217

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	0.41179777510732885	0.4153218822924927
Synthetic AUC	0.498313988877704	0.49838673730065575
X-intercept	0.01902049159058337	0.01892468052999485
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5113136894044943	0.5066628608384266
Synthetic Elbow Point	0.5029270752100471	0.5001809639186293
JS Distance	0.04643248851796976	0.04203742747657625
Synthetic JS Distance	0.12973860412075608	0.12560334133460488
% Genome Enriched	45.07650912400746	45.00524964769475
Diff. Enrichment	8.826607213439742	8.299143536152243
CHANCE Divergence	0.0751174023032103	0.07059970928337847

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	0.5318017841650482	0.5361294905629885	0.4434942544843049	0.4290894928429614	0.4350954134236024	0.42747008629817507	0.5174836297018545	0.5340125020851535	0.5335114048221883

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	0.35870361938519624	0.21725192226063933	0.20972614577543586	0.35935865221013585

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	0.009720899988526634	0.003914028014858186	0.004459020418823811	0.010097834211329234

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