QC Report

	general
Report generated at	2021-08-30 21:21:18
Title	lin-29_RW12227_L4larva_1_2
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	12140830	10809904	14719590
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11630341	10286300	14063499
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	95.8	95.19999999999999	95.5
Paired Reads	12140830	10809904	14719590
Paired Reads (QC-failed)	0	0	0
Read1	6070415	5404952	7359795
Read1 (QC-failed)	0	0	0
Read2	6070415	5404952	7359795
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11591518	10249244	13973232
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	95.5	94.8	94.89999999999999
With itself	11623494	10280442	14056972
With itself (QC-failed)	0	0	0
Singletons	6847	5858	6527
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.0
Diff. Chroms	4418	3999	22702
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5318806	4699016	6386922
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	867802	807338	1166272
Paired Optical Duplicate Reads	42394	40703	60935
% Duplicate Reads	16.3157	17.180999999999997	18.260299999999997

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	8902008	7783356	10441300
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8902008	7783356	10441300
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8902008	7783356	10441300
Paired Reads (QC-failed)	0	0	0
Read1	4451004	3891678	5220650
Read1 (QC-failed)	0	0	0
Read2	4451004	3891678	5220650
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8902008	7783356	10441300
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8902008	7783356	10441300
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	5275649	4662452	6305656
Distinct Fragments	4415835	3862236	5156637
Positions with Two Read	645470	590299	828974
NRF = Distinct/Total	0.837022	0.82837	0.81778
PBC1 = OneRead/Distinct	0.831208	0.821931	0.810555
PBC2 = OneRead/TwoRead	5.68652	5.377766	5.042059

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	43668	841
N1	31271	534
N2	31712	387
Np	43644	906
N optimal	43668	906
N conservative	43668	841
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0005499037668408	1.0772889417360285
Self Consistency Ratio	1.0141025231044738	1.37984496124031
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	85047	86007

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	68.0	72.0	72.0
25 percentile	264.0	270.0	290.0	290.0
50 percentile (median)	264.0	270.0	290.0	290.0
75 percentile	264.0	270.0	290.0	290.0
Max size	292.0	270.0	480.0	480.0
Mean	263.92192552353407	269.9407490088016	276.18101545253865	289.71093249061096

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4977958	4399135
Estimated Fragment Length	175	185
Cross-correlation at Estimated Fragment Length	0.591171351284087	0.556365210808887
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5912658	0.5565712
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5864042	0.55215
NSC (Normalized Strand Cross-correlation coeff.)	1.008129	1.007634
RSC (Relative Strand Cross-correlation coeff.)	0.9805689	0.9534084

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	0.39851403292276116	0.39934405489022606
Synthetic AUC	0.49786380143510106	0.4977164805176501
X-intercept	0.019699194713361054	0.020046369825295098
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5440134241043281	0.5342206916366713
Synthetic Elbow Point	0.49850354135837766	0.49863223045897215
JS Distance	0.05437960631357901	0.05087861096549434
Synthetic JS Distance	0.15317194489010358	0.1499778461437792
% Genome Enriched	42.4714877451176	43.0227778797577
Diff. Enrichment	10.47746429219486	10.492979483153603
CHANCE Divergence	0.08908063591318093	0.08923166988658256

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	0.40140651412580175	0.41261532942859097	0.4047619368573922	0.4240533260973801	0.408909315740898	0.42930401744440316	0.5285001274170584	0.40482293344034925	0.4065637405333201

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	0.22365355649418256	0.17014767904050412	0.1731755556343562	0.2239135448288692

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	0.010413198057890736	0.008077054075889396	0.005850946558271265	0.01095115455677203

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