QC Report

	general
Report generated at	2021-08-30 13:44:08
Title	fkh-7_PS9154_L1larva_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	12584500	20299114	19326670
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11890041	19116206	17779943
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	94.5	94.19999999999999	92.0
Paired Reads	12584500	20299114	19326670
Paired Reads (QC-failed)	0	0	0
Read1	6292250	10149557	9663335
Read1 (QC-failed)	0	0	0
Read2	6292250	10149557	9663335
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11817752	19042316	17644938
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	93.89999999999999	93.8	91.3
With itself	11882448	19098040	17761746
With itself (QC-failed)	0	0	0
Singletons	7593	18166	18197
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4118	6347	23531
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	5451165	8790794	8103282
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	877422	1114046	1106428
Paired Optical Duplicate Reads	42974	68195	70388
% Duplicate Reads	16.096	12.6729	13.6541

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	9147486	15353496	13993708
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9147486	15353496	13993708
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9147486	15353496	13993708
Paired Reads (QC-failed)	0	0	0
Read1	4573743	7676748	6996854
Read1 (QC-failed)	0	0	0
Read2	4573743	7676748	6996854
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9147486	15353496	13993708
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9147486	15353496	13993708
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	5440124	8775762	8020262
Distinct Fragments	4557479	7659705	6923378
Positions with Two Read	658460	895042	866127
NRF = Distinct/Total	0.837753	0.872825	0.863236
PBC1 = OneRead/Distinct	0.83356	0.869924	0.859492
PBC2 = OneRead/TwoRead	5.769421	7.444744	6.870342

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	55758	737
N1	30160	659
N2	40810	351
Np	85065	866
N optimal	85065	866
N conservative	55758	737
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.5256106747013882	1.175033921302578
Self Consistency Ratio	1.3531167108753315	1.8774928774928774
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	76025	141249

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	62.0	78.0	80.0	80.0
25 percentile	250.0	310.0	320.0	320.0
50 percentile (median)	250.0	310.0	320.0	320.0
75 percentile	250.0	310.0	320.0	320.0
Max size	250.0	310.0	457.0	457.0
Mean	249.87613285103583	309.9610475118408	304.1027713625866	319.8381590548404

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5156908	8271276
Estimated Fragment Length	135	170
Cross-correlation at Estimated Fragment Length	0.601503002727529	0.716454938435017
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.602602	0.7173593
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.592149	0.7124277
NSC (Normalized Strand Cross-correlation coeff.)	1.015797	1.005653
RSC (Relative Strand Cross-correlation coeff.)	0.8948671	0.816626

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	0.40337714040241407	0.4217705780811779
Synthetic AUC	0.49789388872467594	0.49837775170091303
X-intercept	0.01953561731352819	0.01840560613320556
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5393048235106213	0.5101002236064527
Synthetic Elbow Point	0.4988499878489845	0.5002284036317267
JS Distance	0.06158839065429264	0.048900832504993066
Synthetic JS Distance	0.14952243749818056	0.1286435798921132
% Genome Enriched	44.36891071713784	46.89346749720492
Diff. Enrichment	8.074462799328469	5.124658121216608
CHANCE Divergence	0.0687556320596504	0.04372091062758088

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	0.3503546220240184	0.593293019387897	0.41824509635869433	0.439717312591217	0.4178324881464674	0.42300672107512194	0.5914660073624805	0.5666933213784393	0.5837393443037788

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	0.26914308985656166	0.1550651184380058	0.20575789383733842	0.39012089392988414

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	0.009079554443981062	0.009876812055246655	0.004640571762939203	0.010199019778064406

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