QC Report

	general
Report generated at	2021-08-31 22:47:34
Title	sea-1_OP129_earlyembryonic_1_3
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	18898082	18546186	18212930
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	18839097	18476370	18162281
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.6	99.7
Paired Reads	18898082	18546186	18212930
Paired Reads (QC-failed)	0	0	0
Read1	9449041	9273093	9106465
Read1 (QC-failed)	0	0	0
Read2	9449041	9273093	9106465
Read2 (QC-failed)	0	0	0
Properly Paired Reads	18732916	18362624	18069638
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.1	99.0	99.2
With itself	18826202	18460228	18148090
With itself (QC-failed)	0	0	0
Singletons	12895	16142	14191
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	11354	8729	8507
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8447861	8289877	8290105
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1086289	1169869	1070944
Paired Optical Duplicate Reads	112894	115768	114888
% Duplicate Reads	12.8587	14.112	12.918299999999999

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	14723144	14240016	14438322
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14723144	14240016	14438322
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14723144	14240016	14438322
Paired Reads (QC-failed)	0	0	0
Read1	7361572	7120008	7219161
Read1 (QC-failed)	0	0	0
Read2	7361572	7120008	7219161
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14723144	14240016	14438322
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14723144	14240016	14438322
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	8408219	8254035	8221278
Distinct Fragments	7329169	7093296	7162517
Positions with Two Read	878234	917411	857784
NRF = Distinct/Total	0.871667	0.859373	0.871217
PBC1 = OneRead/Distinct	0.867228	0.854534	0.866895
PBC2 = OneRead/TwoRead	7.237322	6.607142	7.238595

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	77088	1249
N1	44234	536
N2	43612	556
Np	77093	1241
N optimal	77093	1249
N conservative	77088	1249
Optimal Set	pooled-pr1_vs_pooled-pr2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0000648609381486	1.0064464141821112
Self Consistency Ratio	1.0142621296890764	1.037313432835821
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	121969	122014

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	76.0	73.0	80.0	80.0
25 percentile	304.0	284.0	320.0	320.0
50 percentile (median)	304.0	284.0	320.0	320.0
75 percentile	304.0	284.0	320.0	320.0
Max size	304.0	284.0	320.0	320.0
Mean	303.94665037837484	283.92472175324144	307.2570056044836	319.79524729871713

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7924231	7786667
Estimated Fragment Length	180	170
Cross-correlation at Estimated Fragment Length	0.711115431448821	0.70298389616592
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7111205	0.7029069
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7066849	0.6977573
NSC (Normalized Strand Cross-correlation coeff.)	1.006269	1.00749
RSC (Relative Strand Cross-correlation coeff.)	0.9988557	1.014953

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	0.41349700337158546	0.4086410756954992
Synthetic AUC	0.4983385705517296	0.4983051558199478
X-intercept	0.01848422195435423	0.01867381395237449
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5233297942827037	0.526564832480502
Synthetic Elbow Point	0.5006288187621045	0.4985374702869184
JS Distance	0.037558366999610966	0.04467718995949032
Synthetic JS Distance	0.1338130267892781	0.13923987127228957
% Genome Enriched	43.42574779075429	43.45628208096177
Diff. Enrichment	7.955222057236422	8.559926092150222
CHANCE Divergence	0.06761386112770504	0.07277469740068457

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	0.5291936966723955	0.5181037015688746	0.44024116044779565	0.43596201015504477	0.4452038233138248	0.436064397680452	0.5120256905669133	0.5261942412361083	0.5241154625393085

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	0.3653805385876403	0.2294784999725602	0.22106653531849965	0.3654214871581692

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	0.012263578974117464	0.006490597388709911	0.00676818059754989	0.012230606052654476

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