QC Report

	general
Report generated at	2022-08-01 21:30:23
Title	ceh-5_PHX1592_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	19988666	20388350	19587760
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	19959956	20355869	19560256
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.9	99.8	99.9
Paired Reads	19988666	20388350	19587760
Paired Reads (QC-failed)	0	0	0
Read1	9994333	10194175	9793880
Read1 (QC-failed)	0	0	0
Read2	9994333	10194175	9793880
Read2 (QC-failed)	0	0	0
Properly Paired Reads	19877912	20274764	19490736
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.4	99.4	99.5
With itself	19946090	20339816	19544900
With itself (QC-failed)	0	0	0
Singletons	13866	16053	15356
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	11670	10248	15350
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8963030	9137078	8948666
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1123695	1183091	1113216
Paired Optical Duplicate Reads	65481	68619	71491
% Duplicate Reads	12.537	12.948200000000002	12.44

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	15678670	15907974	15670900
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15678670	15907974	15670900
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	15678670	15907974	15670900
Paired Reads (QC-failed)	0	0	0
Read1	7839335	7953987	7835450
Read1 (QC-failed)	0	0	0
Read2	7839335	7953987	7835450
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15678670	15907974	15670900
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	15678670	15907974	15670900
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	8917749	9096946	8896616
Distinct Fragments	7806238	7924983	7795670
Positions with Two Read	898565	937966	897947
NRF = Distinct/Total	0.87536	0.87117	0.876251
PBC1 = OneRead/Distinct	0.872018	0.867748	0.872426
PBC2 = OneRead/TwoRead	7.57561	7.3317	7.574105

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	74171	2162
N1	32923	1197
N2	33540	1016
Np	73912	2157
N optimal	74171	2162
N conservative	74171	2162
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0035041671176534	1.0023180343069078
Self Consistency Ratio	1.018740697992285	1.1781496062992125
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	111985	114652

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	85.0	84.0	94.0	94.0
25 percentile	340.0	336.0	376.0	376.0
50 percentile (median)	340.0	336.0	376.0	376.0
75 percentile	340.0	336.0	376.0	376.0
Max size	340.0	336.0	376.0	376.0
Mean	339.7201410903246	335.78619649024876	350.1392229417206	375.2496258645562

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	8404693	8574856
Estimated Fragment Length	195	175
Cross-correlation at Estimated Fragment Length	0.723506479502891	0.725779034326844
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7235909	0.7260153
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7186938	0.7210718
NSC (Normalized Strand Cross-correlation coeff.)	1.006696	1.006528
RSC (Relative Strand Cross-correlation coeff.)	0.982759	0.9521971

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	0.4167628056603102	0.41766512662549676
Synthetic AUC	0.49839256102759333	0.4984034855434891
X-intercept	0.01838313096184023	0.018291295164246327
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5259915271494567	0.5209365654210272
Synthetic Elbow Point	0.500736099563358	0.5007219868325108
JS Distance	0.03925542773011859	0.037364197102982416
Synthetic JS Distance	0.12858996697213962	0.12638481602850135
% Genome Enriched	40.98611682312026	40.87351814954861
Diff. Enrichment	8.253694662705207	8.17728716824116
CHANCE Divergence	0.07020904602313915	0.06957036981205399

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	0.5122490619421163	0.520731678339429	0.374336806076433	0.38284040659855156	0.38656319529184496	0.3812348927946315	0.5000138033024337	0.5177555402523243	0.5170801326130288

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	0.3790026252868143	0.1934106017921163	0.19487094962564058	0.37757015275190364

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	0.022578625320246116	0.014503589909093055	0.012349467003152004	0.02256263755022534

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