QC Report

	general
Report generated at	2021-08-27 17:26:13
Title	aptf-3_OP765_youngadult_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	13335640	13875676	13008706
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	13198903	13749854	12967564
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.0	99.1	99.7
Paired Reads	13335640	13875676	13008706
Paired Reads (QC-failed)	0	0	0
Read1	6667820	6937838	6504353
Read1 (QC-failed)	0	0	0
Read2	6667820	6937838	6504353
Read2 (QC-failed)	0	0	0
Properly Paired Reads	13136086	13669332	12859722
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.5	98.5	98.9
With itself	13190232	13738932	12959292
With itself (QC-failed)	0	0	0
Singletons	8671	10922	8272
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4596	5395	36965
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	6002192	6249164	5867235
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1055676	1069956	923683
Paired Optical Duplicate Reads	68361	68083	59686
% Duplicate Reads	17.5882	17.1216	15.743099999999998

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	9893032	10358416	9887104
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	9893032	10358416	9887104
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	9893032	10358416	9887104
Paired Reads (QC-failed)	0	0	0
Read1	4946516	5179208	4943552
Read1 (QC-failed)	0	0	0
Read2	4946516	5179208	4943552
Read2 (QC-failed)	0	0	0
Properly Paired Reads	9893032	10358416	9887104
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	9893032	10358416	9887104
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	5986305	6219132	5795735
Distinct Fragments	4935405	5157216	4886319
Positions with Two Read	768887	781278	688978
NRF = Distinct/Total	0.824449	0.82925	0.843089
PBC1 = OneRead/Distinct	0.81768	0.823211	0.837874
PBC2 = OneRead/TwoRead	5.248602	5.434016	5.942306

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	74685	675
N1	59937	178
N2	47578	241
Np	75595	785
N optimal	75595	785
N conservative	74685	675
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0121845082680592	1.162962962962963
Self Consistency Ratio	1.259762915633276	1.353932584269663
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	119215	117569

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	68.0	86.0	74.0	74.0
25 percentile	270.0	290.0	296.0	296.0
50 percentile (median)	270.0	290.0	296.0	296.0
75 percentile	270.0	290.0	296.0	296.0
Max size	270.0	290.0	296.0	296.0
Mean	269.99519355785765	289.9934251375788	293.74140127388534	295.97654606786165

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	5643157	5872415
Estimated Fragment Length	160	175
Cross-correlation at Estimated Fragment Length	0.616694077751432	0.627088298710726
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.615285	0.6264103
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6097942	0.6217089
NSC (Normalized Strand Cross-correlation coeff.)	1.011315	1.008653
RSC (Relative Strand Cross-correlation coeff.)	1.256634	1.144214

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	0.39112739785861383	0.3975342381041549
Synthetic AUC	0.49797788433066814	0.49802385929377474
X-intercept	0.019382405358101516	0.01903115913250165
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5000169635961227	0.5124682431501997
Synthetic Elbow Point	0.5015185215206792	0.502247835265171
JS Distance	0.07597142560352656	0.057432362055687414
Synthetic JS Distance	0.15931365321361232	0.15049573374386824
% Genome Enriched	46.76903365377899	44.28296874906451
Diff. Enrichment	11.772229303922732	10.802007657339235
CHANCE Divergence	0.10081176910265234	0.09198414549679942

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	0.5398112530112104	0.5379048302365922	0.543769594599512	0.48361351774248107	0.5427003571806904	0.47801285447504716	0.5272553844051052	0.5399434154041726	0.5387799430440727

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	0.36666484292876245	0.3042827517387996	0.25669146711234614	0.370690530375902

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	0.006749838332547875	0.002337200567025357	0.0031237401548653773	0.007629133482208284

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