QC Report

	general
Report generated at	2021-08-30 23:38:55
Title	lin-38_RW12236_L4larva_2_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	41183196	44791230	35412338
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	39246420	42185829	35134064
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	95.3	94.19999999999999	99.2
Paired Reads	41183196	44791230	35412338
Paired Reads (QC-failed)	0	0	0
Read1	20591598	22395615	17706169
Read1 (QC-failed)	0	0	0
Read2	20591598	22395615	17706169
Read2 (QC-failed)	0	0	0
Properly Paired Reads	39120320	42038194	34663800
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	95.0	93.89999999999999	97.89999999999999
With itself	39215774	42153946	35106942
With itself (QC-failed)	0	0	0
Singletons	30646	31883	27122
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	7535	7802	219983
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	17927183	19225819	15557873
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2851999	3272632	1880894
Paired Optical Duplicate Reads	158743	173964	161779
% Duplicate Reads	15.908800000000001	17.022100000000002	12.0897

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	30150368	31906374	27353958
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	30150368	31906374	27353958
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	30150368	31906374	27353958
Paired Reads (QC-failed)	0	0	0
Read1	15075184	15953187	13676979
Read1 (QC-failed)	0	0	0
Read2	15075184	15953187	13676979
Read2 (QC-failed)	0	0	0
Properly Paired Reads	30150368	31906374	27353958
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	30150368	31906374	27353958
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	17711294	18962489	15415623
Distinct Fragments	14927992	15793241	13563564
Positions with Two Read	2088381	2310081	1536587
NRF = Distinct/Total	0.842852	0.832868	0.879858
PBC1 = OneRead/Distinct	0.838521	0.828709	0.87571
PBC2 = OneRead/TwoRead	5.993849	5.6656	7.729953

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	44228	5431
N1	41662	4455
N2	42156	4501
Np	44565	5577
N optimal	44565	5577
N conservative	44228	5431
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.007619607488469	1.026882710366415
Self Consistency Ratio	1.0118573280207384	1.0103254769921437
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	64973	66006

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	90.0	84.0	94.0	94.0
25 percentile	360.0	336.0	263.0	376.0
50 percentile (median)	360.0	336.0	376.0	376.0
75 percentile	360.0	336.0	376.0	376.0
Max size	1596.0	1746.0	1742.0	1742.0
Mean	356.8332538131224	333.3061994364149	340.3188093957325	371.2232020644003

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	160	140
Cross-correlation at Estimated Fragment Length	0.817083337390419	0.817287117471362
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.8100484	0.8112419
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7949408	0.7960078
NSC (Normalized Strand Cross-correlation coeff.)	1.027854	1.026733
RSC (Relative Strand Cross-correlation coeff.)	1.465659	1.396818

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	0.37253361756473774	0.3741600553540664
Synthetic AUC	0.4988271722027435	0.4988523551438666
X-intercept	0.01879564778642581	0.01893152956927473
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6725408894261992	0.6672295103260164
Synthetic Elbow Point	0.500350781580908	0.5013098756691835
JS Distance	0.12451465411996333	0.11862099314460785
Synthetic JS Distance	0.21357513921881124	0.21045333532196336
% Genome Enriched	19.38893162948235	18.710521845993984
Diff. Enrichment	11.979583294831308	11.605819820241347
CHANCE Divergence	0.11186420151676223	0.10936834287827259

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	0.3580538386795146	0.35149707077338216	0.38732038030182586	0.3783921433132989	0.38898390891945334	0.3793065535624044	0.3358268792132207	0.3523489082830385	0.35485167284004926

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	0.28329988706142517	0.27838535834786493	0.27056578099410483	0.2846237722244587

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	0.1010986203561895	0.09281283067589756	0.0897086895552594	0.10209111525706586

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