QC Report

	general
Report generated at	2023-04-20 15:41:44
Title	sma-3_CS152_youngadult_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	12651490	12476730	12770438
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12450660	12298799	12629186
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.4	98.6	98.9
Paired Reads	12651490	12476730	12770438
Paired Reads (QC-failed)	0	0	0
Read1	6325745	6238365	6385219
Read1 (QC-failed)	0	0	0
Read2	6325745	6238365	6385219
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12284720	12128614	12469074
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.1	97.2	97.6
With itself	12440286	12287746	12617992
With itself (QC-failed)	0	0	0
Singletons	10374	11053	11194
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	12274	12134	91254
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5520246	5461799	5657823
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	792432	822185	798161
Paired Optical Duplicate Reads	46011	48636	50277
% Duplicate Reads	14.355	15.0534	14.1072

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	9455628	9279228	9719324
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9455628	9279228	9719324
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9455628	9279228	9719324
Paired Reads (QC-failed)	0	0	0
Read1	4727814	4639614	4859662
Read1 (QC-failed)	0	0	0
Read2	4727814	4639614	4859662
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9455628	9279228	9719324
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9455628	9279228	9719324
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	5492910	5424721	5613690
Distinct Fragments	4705984	4610500	4824036
Positions with Two Read	610008	625569	624458
NRF = Distinct/Total	0.856738	0.849905	0.859334
PBC1 = OneRead/Distinct	0.852783	0.845177	0.854448
PBC2 = OneRead/TwoRead	6.578902	6.229028	6.600742

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	66267	736
N1	33539	271
N2	30870	288
Np	65204	742
N optimal	66267	742
N conservative	66267	736
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0163026808171278	1.0081521739130435
Self Consistency Ratio	1.0864593456430192	1.062730627306273
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	104567	119019

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	82.0	79.0	81.0	81.0
25 percentile	310.0	310.0	324.0	324.0
50 percentile (median)	310.0	310.0	324.0	324.0
75 percentile	310.0	310.0	324.0	324.0
Max size	310.0	310.0	324.0	324.0
Mean	309.98709918042977	309.987052487418	319.6280323450135	323.95104652391086

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5227043	5171435
Estimated Fragment Length	185	175
Cross-correlation at Estimated Fragment Length	0.608424334161665	0.603577029065918
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6075414	0.6028509
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6031414	0.5983737
NSC (Normalized Strand Cross-correlation coeff.)	1.008759	1.008696
RSC (Relative Strand Cross-correlation coeff.)	1.200672	1.162184

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	0.4046117313561212	0.4040417254127062
Synthetic AUC	0.4979223196166952	0.4979044189014187
X-intercept	0.018926626394701183	0.018693136802948755
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5238329012778067	0.5270658340866865
Synthetic Elbow Point	0.49803072395498954	0.4988831991587154
JS Distance	0.036517027000289866	0.034118985928917454
Synthetic JS Distance	0.14465317938304956	0.14766917985540043
% Genome Enriched	44.32550444727825	43.88207378670227
Diff. Enrichment	9.46194091943614	9.558811016860197
CHANCE Divergence	0.08051602934242084	0.08130888110183557

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	0.4922377445474801	0.5383677392127879	0.42024030556193626	0.40962028306665166	0.41580041008381463	0.41393249524637177	0.5435777035062346	0.47732483238728923	0.5436335352670979

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	0.3269802020362473	0.18920298048950318	0.17649927343093627	0.3225858261200406

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	0.0079875714016697	0.003574484952242199	0.003825641529661735	0.007949994384798048

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