QC Report

	general
Report generated at	2021-09-12 15:18:12
Title	tag-97_OP719_L4larva_1_1
Description	mkudron
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	11628786	13666544	14090776
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11558474	13569210	13929471
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	99.3	98.9
Paired Reads	11628786	13666544	14090776
Paired Reads (QC-failed)	0	0	0
Read1	5814393	6833272	7045388
Read1 (QC-failed)	0	0	0
Read2	5814393	6833272	7045388
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11515084	13520310	13859974
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	98.9	98.4
With itself	11550560	13558076	13916780
With itself (QC-failed)	0	0	0
Singletons	7914	11134	12691
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	3607	5275	17547
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5304151	6223740	6393838
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	601133	811463	864953
Paired Optical Duplicate Reads	49925	67655	81163
% Duplicate Reads	11.3333	13.0382	13.5279

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	9406036	10824554	11057770
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9406036	10824554	11057770
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9406036	10824554	11057770
Paired Reads (QC-failed)	0	0	0
Read1	4703018	5412277	5528885
Read1 (QC-failed)	0	0	0
Read2	4703018	5412277	5528885
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9406036	10824554	11057770
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9406036	10824554	11057770
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	5270913	6187063	6311551
Distinct Fragments	4676066	5385160	5464305
Positions with Two Read	488980	636811	670899
NRF = Distinct/Total	0.887145	0.87039	0.865763
PBC1 = OneRead/Distinct	0.884684	0.867312	0.862016
PBC2 = OneRead/TwoRead	8.460144	7.334382	7.020906

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	80723	182
N1	44654	70
N2	44263	71
Np	85780	321
N optimal	85780	321
N conservative	80723	182
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0626463337586562	1.7637362637362637
Self Consistency Ratio	1.0088335630210334	1.0142857142857142
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	116884	142985

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	111.0	260.0	74.0	74.0
25 percentile	436.0	260.0	296.0	296.0
50 percentile (median)	436.0	260.0	296.0	296.0
75 percentile	436.0	260.0	296.0	296.0
Max size	436.0	260.0	296.0	296.0
Mean	435.96948256390954	260.0	292.4828660436137	295.98683842387504

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4983121	5849599
Estimated Fragment Length	75	175
Cross-correlation at Estimated Fragment Length	0.615391580390802	0.644982190196372
Phantom Peak	50	55
Cross-correlation at Phantom Peak	0.6163103	0.6454135
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6117042	0.6411943
NSC (Normalized Strand Cross-correlation coeff.)	1.006028	1.005908
RSC (Relative Strand Cross-correlation coeff.)	0.8005494	0.8977831

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	0.407140592386342	0.4104560606097409
Synthetic AUC	0.49792554851931836	0.49806720540887084
X-intercept	0.019257399861919794	0.019079811157359555
Synthetic X-intercept	0.0	0.0
Elbow Point	0.528891088239637	0.5251178271124076
Synthetic Elbow Point	0.5031723014614222	0.5030631772180139
JS Distance	0.032014508260884034	0.03215549840465402
Synthetic JS Distance	0.13957755744362252	0.13554827654155854
% Genome Enriched	47.238395875153145	48.26781174799165
Diff. Enrichment	7.784973675902002	7.38794510972971
CHANCE Divergence	0.06659453954034635	0.06331271287005485

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	0.5812606926020696	0.5728218455928993	0.5082211039804653	0.4657053832046321	0.4828778031468304	0.4540625792180591	0.5836203491840821	0.5780374593091492	0.5790599857997207

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	0.3574033678701412	0.2610826707446155	0.20718673489919306	0.3826185494342973

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	0.0019753749149184477	0.0010854732004002537	0.0008599892429748144	0.003226944938333484

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