QC Report

	general
Report generated at	2023-07-21 17:02:15
Title	ttx-1_PHX1679_lateembryonic_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	5962876	11073042	10631530
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	5946702	11044934	10603229
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.7	99.7
Paired Reads	5962876	11073042	10631530
Paired Reads (QC-failed)	0	0	0
Read1	2981438	5536521	5315765
Read1 (QC-failed)	0	0	0
Read2	2981438	5536521	5315765
Read2 (QC-failed)	0	0	0
Properly Paired Reads	5897000	10971138	10524196
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.9	99.1	99.0
With itself	5937734	11028490	10581786
With itself (QC-failed)	0	0	0
Singletons	8968	16444	21443
Singletons (QC-failed)	0	0	0
% Singleton	0.2	0.1	0.2
Diff. Chroms	3954	7214	10551
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	2691328	5017462	4834705
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	283239	496578	491482
Paired Optical Duplicate Reads	20648	37129	38522
% Duplicate Reads	10.5241	9.897	10.1657

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	4816178	9041768	8686446
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	4816178	9041768	8686446
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	4816178	9041768	8686446
Paired Reads (QC-failed)	0	0	0
Read1	2408089	4520884	4343223
Read1 (QC-failed)	0	0	0
Read2	2408089	4520884	4343223
Read2 (QC-failed)	0	0	0
Properly Paired Reads	4816178	9041768	8686446
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	4816178	9041768	8686446
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	2677645	4999427	4804761
Distinct Fragments	2397592	4508033	4320167
Positions with Two Read	235697	419453	411881
NRF = Distinct/Total	0.895411	0.90171	0.899143
PBC1 = OneRead/Distinct	0.892841	0.899317	0.896572
PBC2 = OneRead/TwoRead	9.082288	9.665326	9.404024

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	35750	911
N1	23732	468
N2	29456	518
Np	34075	960
N optimal	35750	960
N conservative	35750	911
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.049156272927366	1.0537870472008781
Self Consistency Ratio	1.241193325467723	1.106837606837607
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	59805	80687

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	81.0	85.0	91.0	91.0
25 percentile	324.0	340.0	360.0	360.0
50 percentile (median)	324.0	340.0	360.0	360.0
75 percentile	324.0	340.0	360.0	360.0
Max size	324.0	340.0	360.0	360.0
Mean	323.9351893654377	339.9307571232045	349.91979166666664	359.7293146853147

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	2535146	4730228
Estimated Fragment Length	185	190
Cross-correlation at Estimated Fragment Length	0.454912655881873	0.608102344084419
Phantom Peak	45	50
Cross-correlation at Phantom Peak	0.4555094	0.6085695
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.4487941	0.6036524
NSC (Normalized Strand Cross-correlation coeff.)	1.013633	1.007372
RSC (Relative Strand Cross-correlation coeff.)	0.9111374	0.9049987

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	0.3871267142776628	0.4034003881746671
Synthetic AUC	0.4971014879659105	0.4978850022542687
X-intercept	0.020160276492914072	0.019046801853396498
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5363595365710568	0.5233709945842828
Synthetic Elbow Point	0.5006313307666362	0.5030177959594719
JS Distance	0.05976048781661059	0.03924915363029519
Synthetic JS Distance	0.16158233893610222	0.14033483675825345
% Genome Enriched	41.947862248420584	43.09306492874161
Diff. Enrichment	12.468758327510471	9.807794243989093
CHANCE Divergence	0.10606308889453862	0.08339342385122725

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	0.36400710272751546	0.43347595293309893	0.44301209672395964	0.4013531424385142	0.43646079379158903	0.3936314225270987	0.5568489009843162	0.3837530635848828	0.37324512207582883

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	0.2173827203540842	0.16608418542670142	0.1867996391856106	0.21085917061590512

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	0.012003726959247785	0.008611807952280833	0.0076835636570192906	0.012586497306310762

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