QC Report

	general
Report generated at	2023-04-20 15:42:25
Title	sma-4_CS692_youngadult_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	14277526	14008294	14035786
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14144120	13773774	13975926
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.1	98.3	99.6
Paired Reads	14277526	14008294	14035786
Paired Reads (QC-failed)	0	0	0
Read1	7138763	7004147	7017893
Read1 (QC-failed)	0	0	0
Read2	7138763	7004147	7017893
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13975644	13552364	13658112
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.89999999999999	96.7	97.3
With itself	14134746	13763350	13964140
With itself (QC-failed)	0	0	0
Singletons	9374	10424	11786
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	18998	16731	200090
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6262238	6067464	6134812
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1064924	992847	846194
Paired Optical Duplicate Reads	65601	60887	53279
% Duplicate Reads	17.0055	16.363500000000002	13.7933

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	10394628	10149234	10577236
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	10394628	10149234	10577236
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	10394628	10149234	10577236
Paired Reads (QC-failed)	0	0	0
Read1	5197314	5074617	5288618
Read1 (QC-failed)	0	0	0
Read2	5197314	5074617	5288618
Read2 (QC-failed)	0	0	0
Properly Paired Reads	10394628	10149234	10577236
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	10394628	10149234	10577236
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	6241071	6041094	6086658
Distinct Fragments	5182384	5055631	5252550
Positions with Two Read	786689	739130	660936
NRF = Distinct/Total	0.830368	0.836873	0.862961
PBC1 = OneRead/Distinct	0.823841	0.831155	0.858642
PBC2 = OneRead/TwoRead	5.427124	5.685077	6.823744

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	19649	5378
N1	17718	4143
N2	17700	3903
Np	19589	5357
N optimal	19649	5378
N conservative	19649	5378
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0030629434886926	1.003920104536121
Self Consistency Ratio	1.0010169491525425	1.0614911606456572
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	36510	35071

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	100.0	98.0	104.0	104.0
25 percentile	400.0	390.0	284.0	416.0
50 percentile (median)	400.0	390.0	416.0	416.0
75 percentile	400.0	390.0	416.0	416.0
Max size	705.0	674.0	913.0	913.0
Mean	393.74869898657903	384.5812209517835	356.93547787281517	399.4270955264899

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5937517	5774470
Estimated Fragment Length	205	195
Cross-correlation at Estimated Fragment Length	0.630907534974062	0.628504301091838
Phantom Peak	55	55
Cross-correlation at Phantom Peak	0.622799	0.6206333
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6110865	0.6101858
NSC (Normalized Strand Cross-correlation coeff.)	1.032436	1.030021
RSC (Relative Strand Cross-correlation coeff.)	1.6923	1.75339

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	0.3663003128796887	0.3714570675552644
Synthetic AUC	0.4980206664652786	0.49799610100761027
X-intercept	0.01902791026249935	0.018852298715241887
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6512474406612573	0.6453604626566036
Synthetic Elbow Point	0.49917558630836734	0.5008771210369785
JS Distance	0.1208501632229238	0.11197220741284525
Synthetic JS Distance	0.20555624033180697	0.19886079656335737
% Genome Enriched	28.889895551041096	28.959541494214797
Diff. Enrichment	14.638978465393926	14.100894880063075
CHANCE Divergence	0.12756016884659496	0.12311438289089904

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	0.29281432678495084	0.2773783716091283	0.31940248366752516	0.3210312579193153	0.3191852560765041	0.31244137487447327	0.2879942437308039	0.29305314715868447	0.27722024974858667

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	0.19162799088116927	0.18697263625018615	0.1794985710251631	0.19143912668416485

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	0.08895907692526361	0.07685931617754864	0.07127651209933676	0.08873214783082169

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