QC Report

	general
Report generated at	2022-05-06 20:23:26
Title	F37B4.10_OP374_youngadult_1_2
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	14300870	18287190	12191298
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14241564	18225130	12169807
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.7	99.8
Paired Reads	14300870	18287190	12191298
Paired Reads (QC-failed)	0	0	0
Read1	7150435	9143595	6095649
Read1 (QC-failed)	0	0	0
Read2	7150435	9143595	6095649
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14199618	18174736	12121116
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.4	99.4
With itself	14234746	18217034	12164264
With itself (QC-failed)	0	0	0
Singletons	6818	8096	5543
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	6141	7303	9094
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6467299	8280231	5546370
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	886326	1071301	645787
Paired Optical Duplicate Reads	27855	36164	24286
% Duplicate Reads	13.7047	12.9381	11.6434

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	11161946	14417860	9801166
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11161946	14417860	9801166
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	11161946	14417860	9801166
Paired Reads (QC-failed)	0	0	0
Read1	5580973	7208930	4900583
Read1 (QC-failed)	0	0	0
Read2	5580973	7208930	4900583
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11161946	14417860	9801166
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	11161946	14417860	9801166
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	6438247	8237965	5504695
Distinct Fragments	5557286	7174792	4864739
Positions with Two Read	690491	845757	525461
NRF = Distinct/Total	0.863168	0.870942	0.883744
PBC1 = OneRead/Distinct	0.859656	0.867879	0.880801
PBC2 = OneRead/TwoRead	6.918777	7.362462	8.154491

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	89031	843
N1	39178	81
N2	42688	99
Np	91255	947
N optimal	91255	947
N conservative	89031	843
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0249800631240804	1.1233689205219455
Self Consistency Ratio	1.0895910970442595	1.2222222222222223
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	131875	142798

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	65.0	95.0	73.0	73.0
25 percentile	260.0	260.0	276.0	276.0
50 percentile (median)	260.0	260.0	276.0	276.0
75 percentile	260.0	260.0	276.0	276.0
Max size	260.0	260.0	276.0	276.0
Mean	259.99710331753556	259.99671564027506	274.5311510031679	275.9847569996165

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6059331	7756047
Estimated Fragment Length	165	155
Cross-correlation at Estimated Fragment Length	0.649304602300009	0.706066554427
Phantom Peak	55	50
Cross-correlation at Phantom Peak	0.648974	0.7057978
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6448427	0.7018804
NSC (Normalized Strand Cross-correlation coeff.)	1.006919	1.005964
RSC (Relative Strand Cross-correlation coeff.)	1.080028	1.06861

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	0.40788320594703575	0.41577541021836706
Synthetic AUC	0.4980923311367145	0.4983213056883412
X-intercept	0.019109106512064183	0.018817730057676573
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5112319635979005	0.5016444808110643
Synthetic Elbow Point	0.49959009835168144	0.5019968324677345
JS Distance	0.033614557880413815	0.021516010990748933
Synthetic JS Distance	0.13545842685490783	0.12712413869592273
% Genome Enriched	43.75436565749297	44.615123635420204
Diff. Enrichment	9.418195829251868	8.123446506827076
CHANCE Divergence	0.08008652757261539	0.06908063378545287

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	0.5472539465788493	0.5670897761526329	0.4206946672749237	0.41323691588072015	0.42010047712118964	0.41564975662130166	0.5599150361030885	0.563032294847561	0.5619409749973064

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	0.38347976524919697	0.19453167037360689	0.20092107982738075	0.3911981193289738

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	0.006672294543594271	0.0011039293685885956	0.001238741394353947	0.007282346081905391

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