QC Report

	general
Report generated at	2021-08-30 21:32:11
Title	lim-7_OP779_L4larva_1_4
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	33930364	32881304	49549436
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	31315932	31919502	49446426
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	92.30000000000001	97.1	99.8
Paired Reads	33930364	32881304	49549436
Paired Reads (QC-failed)	0	0	0
Read1	16965182	16440652	24774718
Read1 (QC-failed)	0	0	0
Read2	16965182	16440652	24774718
Read2 (QC-failed)	0	0	0
Properly Paired Reads	31183896	31848718	49227468
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	91.9	96.89999999999999	99.4
With itself	31297970	31903020	49419536
With itself (QC-failed)	0	0	0
Singletons	17962	16482	26890
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5120	4723	69348
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	14183961	14508432	22654393
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	2154514	2200154	3212236
Paired Optical Duplicate Reads	77422	80136	150417
% Duplicate Reads	15.1898	15.1647	14.1793

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	24058894	24616556	38884314
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	24058894	24616556	38884314
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	24058894	24616556	38884314
Paired Reads (QC-failed)	0	0	0
Read1	12029447	12308278	19442157
Read1 (QC-failed)	0	0	0
Read2	12029447	12308278	19442157
Read2 (QC-failed)	0	0	0
Properly Paired Reads	24058894	24616556	38884314
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	24058894	24616556	38884314
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	14055201	14381940	22406265
Distinct Fragments	11934993	12230541	19254251
Positions with Two Read	1601219	1643838	2478370
NRF = Distinct/Total	0.849151	0.85041	0.859324
PBC1 = OneRead/Distinct	0.846034	0.846302	0.854849
PBC2 = OneRead/TwoRead	6.306079	6.296689	6.641253

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	64220	1649
N1	46468	883
N2	54012	920
Np	64714	1804
N optimal	64714	1804
N conservative	64220	1649
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0076923076923077	1.0939963614311705
Self Consistency Ratio	1.1623482826891625	1.0419026047565119
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	115412	106793

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	59.0	61.0	66.0	66.0
25 percentile	236.0	244.0	264.0	264.0
50 percentile (median)	236.0	244.0	264.0	264.0
75 percentile	236.0	244.0	264.0	264.0
Max size	485.0	246.0	1286.0	1286.0
Mean	235.80712577548263	243.75044244472952	237.82427937915742	263.26940074790616

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	13176792	13518857
Estimated Fragment Length	130	130
Cross-correlation at Estimated Fragment Length	0.796349069206316	0.800386705274937
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7962551	0.8001638
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7903043	0.7937855
NSC (Normalized Strand Cross-correlation coeff.)	1.007649	1.008316
RSC (Relative Strand Cross-correlation coeff.)	1.015785	1.034951

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	0.4109879876805608	0.4065316642809877
Synthetic AUC	0.4986668367493617	0.4986818213777581
X-intercept	0.018874074192567945	0.018956057140114856
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5103178538863916	0.5092940668340985
Synthetic Elbow Point	0.5010704934710861	0.5006359758505656
JS Distance	0.05412645976015304	0.061119568465228355
Synthetic JS Distance	0.14067289426956853	0.14564916305621423
% Genome Enriched	42.125237950506296	43.24440516372594
Diff. Enrichment	8.066028815019427	8.754849229838896
CHANCE Divergence	0.06854426525473556	0.07442980488152064

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	0.4479243725833781	0.4322369465493061	0.41004741032173714	0.43535188269228237	0.4124698676896675	0.45041897818687554	0.4035408609473564	0.4412171046711595	0.4389063250121499

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	0.28150778267073034	0.20436936959778784	0.24064560452729455	0.2834443030316104

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	0.013200699736725597	0.00809621589421359	0.008522963163490457	0.01417036719742704

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