QC Report

	general
Report generated at	2021-08-31 22:22:47
Title	sox-2_RW12244_lateembryonic_1_2
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	11139782	10854018	12030202
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	11121329	10829515	12014626
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.8	99.8	99.9
Paired Reads	11139782	10854018	12030202
Paired Reads (QC-failed)	0	0	0
Read1	5569891	5427009	6015101
Read1 (QC-failed)	0	0	0
Read2	5569891	5427009	6015101
Read2 (QC-failed)	0	0	0
Properly Paired Reads	11024758	10680848	11866270
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	98.4	98.6
With itself	11113610	10822206	12005098
With itself (QC-failed)	0	0	0
Singletons	7719	7309	9528
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5563	5209	7341
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	4996648	4831854	5440603
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	845619	779877	921506
Paired Optical Duplicate Reads	43208	36441	52073
% Duplicate Reads	16.9237	16.1403	16.9376

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	8302058	8103954	9038194
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8302058	8103954	9038194
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	8302058	8103954	9038194
Paired Reads (QC-failed)	0	0	0
Read1	4151029	4051977	4519097
Read1 (QC-failed)	0	0	0
Read2	4151029	4051977	4519097
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8302058	8103954	9038194
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	8302058	8103954	9038194
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	4967291	4803318	5410851
Distinct Fragments	4127652	4029263	4495889
Positions with Two Read	623986	581871	681030
NRF = Distinct/Total	0.830966	0.83885	0.830902
PBC1 = OneRead/Distinct	0.824549	0.833409	0.824297
PBC2 = OneRead/TwoRead	5.454372	5.771082	5.441681

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	7980	651
N1	19846	571
N2	20317	582
Np	7934	677
N optimal	7980	677
N conservative	7980	651
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0057978321149483	1.0399385560675882
Self Consistency Ratio	1.02373274211428	1.0192644483362523
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	34631	34475

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	69.0	62.0	71.0	71.0
25 percentile	276.0	250.0	284.0	284.0
50 percentile (median)	276.0	250.0	284.0	284.0
75 percentile	276.0	250.0	284.0	284.0
Max size	276.0	250.0	284.0	284.0
Mean	275.84046085876815	249.88977519941986	267.6661742983752	282.5877192982456

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	4714886	4582854
Estimated Fragment Length	165	155
Cross-correlation at Estimated Fragment Length	0.575048052762424	0.571668145344711
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.575171	0.5715959
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5699404	0.5666742
NSC (Normalized Strand Cross-correlation coeff.)	1.008962	1.008813
RSC (Relative Strand Cross-correlation coeff.)	0.9764899	1.014675

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	0.4009927364179	0.39993638690356603
Synthetic AUC	0.497787866018102	0.4977554509557848
X-intercept	0.019779084012721822	0.01998858707146648
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5324809551743265	0.531259851631929
Synthetic Elbow Point	0.5004700369206303	0.5001460537189834
JS Distance	0.04241444971882931	0.04334576694895186
Synthetic JS Distance	0.14630477774280376	0.14731804286909791
% Genome Enriched	42.314230644910275	42.54767691036861
Diff. Enrichment	9.843521405003164	10.01753499610204
CHANCE Divergence	0.08367839148444146	0.08516883485400971

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	0.20037513590003828	0.18919702653790976	0.360094964382334	0.3653447772914858	0.3573165490572456	0.37666338596279936	0.07326247231807462	0.19488131670723716	0.19361029203447908

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	0.05988274298470585	0.12333929731640034	0.1190960610092308	0.05960772185220881

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	0.012269038935239106	0.011358629390447525	0.011215759615614797	0.012369855635848614

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