QC Report

	general
Report generated at	2021-08-29 12:13:52
Title	dmd-8_OP775_L4larva_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	21976076	23236498	22699898
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	21408616	22367385	22587420
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	97.39999999999999	96.3	99.5
Paired Reads	21976076	23236498	22699898
Paired Reads (QC-failed)	0	0	0
Read1	10988038	11618249	11349949
Read1 (QC-failed)	0	0	0
Read2	10988038	11618249	11349949
Read2 (QC-failed)	0	0	0
Properly Paired Reads	21321180	22217364	22443516
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	97.0	95.6	98.9
With itself	21395554	22348658	22573878
With itself (QC-failed)	0	0	0
Singletons	13062	18727	13542
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	4519	5805	62356
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	9731948	10118410	10338249
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1249642	1313443	1338099
Paired Optical Duplicate Reads	80102	83383	103382
% Duplicate Reads	12.840599999999998	12.9807	12.9432

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	16964612	17609934	18000300
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16964612	17609934	18000300
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	16964612	17609934	18000300
Paired Reads (QC-failed)	0	0	0
Read1	8482306	8804967	9000150
Read1 (QC-failed)	0	0	0
Read2	8482306	8804967	9000150
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16964612	17609934	18000300
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	16964612	17609934	18000300
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	9622681	9980686	10202850
Distinct Fragments	8397370	8706903	8890297
Positions with Two Read	976761	1015401	1060485
NRF = Distinct/Total	0.872664	0.872375	0.871354
PBC1 = OneRead/Distinct	0.869765	0.869441	0.867272
PBC2 = OneRead/TwoRead	7.477509	7.45532	7.270543

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	72274	1537
N1	56224	629
N2	49683	545
Np	72796	1556
N optimal	72796	1556
N conservative	72274	1537
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0072225143205025	1.0123617436564736
Self Consistency Ratio	1.131654690739287	1.1541284403669725
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	113396	122947

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	60.0	70.0	70.0
25 percentile	270.0	240.0	280.0	280.0
50 percentile (median)	270.0	240.0	280.0	280.0
75 percentile	270.0	240.0	280.0	280.0
Max size	270.0	240.0	280.0	280.0
Mean	269.95394899290983	239.9695315867813	272.16452442159385	279.8300730809385

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9073631	9416758
Estimated Fragment Length	130	150
Cross-correlation at Estimated Fragment Length	0.73862001475893	0.745295614815638
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7385379	0.7453707
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7335668	0.7404922
NSC (Normalized Strand Cross-correlation coeff.)	1.006889	1.006487
RSC (Relative Strand Cross-correlation coeff.)	1.016517	0.9846086

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	0.4084304373690628	0.4099268692692436
Synthetic AUC	0.49844098651307644	0.4984518668068159
X-intercept	0.018699445106695658	0.018976991595732573
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5236343814207585	0.5207351188158549
Synthetic Elbow Point	0.5009631947140568	0.5015941072490887
JS Distance	0.043691234566637455	0.03964810000504546
Synthetic JS Distance	0.1455726993637976	0.14629872579262848
% Genome Enriched	43.61473352541947	43.01830808458978
Diff. Enrichment	9.731995696307926	9.287670103150624
CHANCE Divergence	0.08273536953674791	0.07894005948277372

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	0.47574804540180465	0.47678855582309393	0.4843718205874676	0.4388006861580871	0.4698356791183907	0.42741970837820387	0.4511651432819971	0.4727457319181729	0.47562993166301776

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	0.3184847604361891	0.26488162535046483	0.22100701797065225	0.3204988432819913

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	0.012337342043479037	0.006500885490337179	0.011099644098609342	0.012410314802109043

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