QC Report

	general
Report generated at	2022-03-18 12:57:30
Title	K11D2.4_RW12320_youngadult_1_1
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	18544554	16732706	20876490
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18466580	16669285	20817219
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.6	99.7
Paired Reads	18544554	16732706	20876490
Paired Reads (QC-failed)	0	0	0
Read1	9272277	8366353	10438245
Read1 (QC-failed)	0	0	0
Read2	9272277	8366353	10438245
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18406786	16616502	20723422
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.3	99.3
With itself	18453532	16658398	20802178
With itself (QC-failed)	0	0	0
Singletons	13048	10887	15041
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6203	4600	29558
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8461716	7634108	9534786
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1365177	1220514	1427731
Paired Optical Duplicate Reads	76805	66367	86901
% Duplicate Reads	16.1336	15.987599999999999	14.9739

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	14193078	12827188	16214110
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14193078	12827188	16214110
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14193078	12827188	16214110
Paired Reads (QC-failed)	0	0	0
Read1	7096539	6413594	8107055
Read1 (QC-failed)	0	0	0
Read2	7096539	6413594	8107055
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14193078	12827188	16214110
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14193078	12827188	16214110
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	8400406	7584141	9420046
Distinct Fragments	7049708	6376792	8015385
Positions with Two Read	1022620	913360	1095439
NRF = Distinct/Total	0.83921	0.840806	0.850886
PBC1 = OneRead/Distinct	0.8332	0.835245	0.845113
PBC2 = OneRead/TwoRead	5.743887	5.831415	6.18374

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	48580	1927
N1	29401	959
N2	30571	1141
Np	50838	1984
N optimal	50838	1984
N conservative	48580	1927
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0464800329353643	1.0295796574987026
Self Consistency Ratio	1.0397945648107207	1.1897810218978102
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	85813	82841

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	74.0	71.0	81.0	81.0
25 percentile	296.0	284.0	324.0	324.0
50 percentile (median)	296.0	284.0	324.0	324.0
75 percentile	296.0	284.0	324.0	324.0
Max size	1026.0	964.0	1352.0	1352.0
Mean	295.75981494645333	283.7113506596975	307.484375	323.2889964200008

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7931185	7156229
Estimated Fragment Length	175	170
Cross-correlation at Estimated Fragment Length	0.700114360223228	0.679652977504919
Phantom Peak	55	50
Cross-correlation at Phantom Peak	0.6994027	0.6784239
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6941541	0.6725622
NSC (Normalized Strand Cross-correlation coeff.)	1.008586	1.010543
RSC (Relative Strand Cross-correlation coeff.)	1.13559	1.209674

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	0.40685744936728147	0.4018635798453371
Synthetic AUC	0.4983094133464806	0.49821864006659217
X-intercept	0.01910179640718563	0.01936926147704591
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5428622754491018	0.5472834331337325
Synthetic Elbow Point	0.49843096393698993	0.4999154269025028
JS Distance	0.06127695466072938	0.06876434659239414
Synthetic JS Distance	0.1457498442090692	0.15039751320338782
% Genome Enriched	40.578842315369265	40.061477045908184
Diff. Enrichment	9.154359521721311	10.004797108310493
CHANCE Divergence	0.07785423979801737	0.08511162366441398

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	0.41457124381335747	0.4025858980159954	0.3688398853525803	0.3723261871580895	0.36196325588618	0.3776890149267322	0.4914400176519358	0.3903768830124113	0.46437059238207296

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	0.2630573288952818	0.16896616787422714	0.1759822963536513	0.272392211090742

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	0.022464952787659455	0.01335820179386036	0.016042331335597484	0.02294666529189609

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