QC Report

	general
Report generated at	2021-08-29 16:42:24
Title	dox-1_RW12180_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	40907006	50739730	41701398
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	39611411	49478699	41442363
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.8	97.5	99.4
Paired Reads	40907006	50739730	41701398
Paired Reads (QC-failed)	0	0	0
Read1	20453503	25369865	20850699
Read1 (QC-failed)	0	0	0
Read2	20453503	25369865	20850699
Read2 (QC-failed)	0	0	0
Properly Paired Reads	39425216	49287204	40968522
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	96.39999999999999	97.1	98.2
With itself	39566970	49418884	41400318
With itself (QC-failed)	0	0	0
Singletons	44441	59815	42045
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	24222	25065	155243
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	17963112	22459626	18740439
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2854357	3539158	2281682
Paired Optical Duplicate Reads	227906	290309	238012
% Duplicate Reads	15.890099999999999	15.7579	12.1752

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	30217510	37840936	32917514
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	30217510	37840936	32917514
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	30217510	37840936	32917514
Paired Reads (QC-failed)	0	0	0
Read1	15108755	18920468	16458757
Read1 (QC-failed)	0	0	0
Read2	15108755	18920468	16458757
Read2 (QC-failed)	0	0	0
Properly Paired Reads	30217510	37840936	32917514
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	30217510	37840936	32917514
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	17888711	22284480	18531679
Distinct Fragments	15130540	18884312	16369321
Positions with Two Read	1976019	2433262	1677702
NRF = Distinct/Total	0.845815	0.84742	0.883316
PBC1 = OneRead/Distinct	0.845798	0.847806	0.8838
PBC2 = OneRead/TwoRead	6.476342	6.579743	8.623225

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	43980	3291
N1	43501	3105
N2	44332	2983
Np	48957	4441
N optimal	48957	4441
N conservative	43980	3291
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1131650750341064	1.3494378608325737
Self Consistency Ratio	1.019103009126227	1.0408984244049615
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	61299	78302

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	110.0	109.0	109.0
25 percentile	404.0	440.0	381.0	436.0
50 percentile (median)	404.0	440.0	436.0	436.0
75 percentile	404.0	440.0	436.0	436.0
Max size	2625.0	2233.0	3411.0	3411.0
Mean	400.86777924599096	438.3170672524329	399.0445845530286	432.2311620401577

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	195	200
Cross-correlation at Estimated Fragment Length	0.814622432654384	0.821888725129631
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.8078389	0.819341
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.8007808	0.8146334
NSC (Normalized Strand Cross-correlation coeff.)	1.017285	1.008906
RSC (Relative Strand Cross-correlation coeff.)	1.961113	1.541184

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	0.3761554950780823	0.4068723250324016
Synthetic AUC	0.4988349026593171	0.4989592789470589
X-intercept	0.01764747015633585	0.01722591279156885
Synthetic X-intercept	0.0	1e-323
Elbow Point	0.5628050546925728	0.5563837970131362
Synthetic Elbow Point	0.500438609924475	0.500041419264936
JS Distance	0.11535371446684847	0.0671868508541955
Synthetic JS Distance	0.1858235978199651	0.14987403987740378
% Genome Enriched	39.81199740272714	36.603766045652065
Diff. Enrichment	13.157857284718338	8.151036783046328
CHANCE Divergence	0.11191492822279062	0.06967982477426293

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	0.364966967827594	0.41291597543993097	0.4068193304597678	0.41113486199178584	0.40949842720319624	0.4082952387858482	0.35355683848555697	0.38411331389749	0.38351934698947865

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	0.2725108063736865	0.29400089550727376	0.27619137116481474	0.2992796808789904

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	0.038888751588597836	0.04046723240928852	0.03454991176751019	0.04982347084445625

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