QC Report

	general
Report generated at	2022-06-01 03:57:16
Title	unc-98_OP85_L1larva_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	16241644	16824016	20279788
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16122957	16722503	19822536
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.3	99.4	97.7
Paired Reads	16241644	16824016	20279788
Paired Reads (QC-failed)	0	0	0
Read1	8120822	8412008	10139894
Read1 (QC-failed)	0	0	0
Read2	8120822	8412008	10139894
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16040714	16645070	19581514
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.8	98.9	96.6
With itself	16111258	16711148	19798266
With itself (QC-failed)	0	0	0
Singletons	11699	11355	24270
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	8690	6519	11471
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7415060	7691316	9082341
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1023937	1093901	1315862
Paired Optical Duplicate Reads	57634	63463	79321
% Duplicate Reads	13.8089	14.222499999999998	14.488100000000001

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	12782246	13194830	15532958
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12782246	13194830	15532958
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12782246	13194830	15532958
Paired Reads (QC-failed)	0	0	0
Read1	6391123	6597415	7766479
Read1 (QC-failed)	0	0	0
Read2	6391123	6597415	7766479
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12782246	13194830	15532958
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12782246	13194830	15532958
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	7393013	7670461	8872175
Distinct Fragments	6373785	6581108	7599292
Positions with Two Read	806034	853316	1002570
NRF = Distinct/Total	0.862136	0.857981	0.856531
PBC1 = OneRead/Distinct	0.857732	0.85342	0.851259
PBC2 = OneRead/TwoRead	6.782595	6.581913	6.452383

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	95243	728
N1	68364	577
N2	70227	394
Np	95631	790
N optimal	95631	790
N conservative	95243	728
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0040737901998047	1.085164835164835
Self Consistency Ratio	1.0272511848341233	1.4644670050761421
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	145921	149110

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	72.0	79.0	79.0
25 percentile	276.0	276.0	316.0	316.0
50 percentile (median)	276.0	276.0	316.0	316.0
75 percentile	276.0	276.0	316.0	316.0
Max size	276.0	276.0	316.0	316.0
Mean	275.9389601222579	275.978874656294	294.9088607594937	315.8257677949619

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6992749	7253323
Estimated Fragment Length	175	180
Cross-correlation at Estimated Fragment Length	0.681333480899272	0.687328450460396
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6811694	0.6873637
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.676748	0.682932
NSC (Normalized Strand Cross-correlation coeff.)	1.006776	1.006438
RSC (Relative Strand Cross-correlation coeff.)	1.037102	0.9920449

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	0.41579117580311775	0.4155607158402876
Synthetic AUC	0.4982230296630093	0.49825053360583627
X-intercept	0.018736400838407028	0.018770336360914262
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5260984130152709	0.5265236051502146
Synthetic Elbow Point	0.49891577719715463	0.49887164768643555
JS Distance	0.07813915948777996	0.07936904854868253
Synthetic JS Distance	0.13134169795891673	0.130693548128035
% Genome Enriched	53.25122267691386	54.621219682603055
Diff. Enrichment	4.39255549884111	4.079586284144171
CHANCE Divergence	0.03845557170938969	0.03601614728065009

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	0.5870263332437821	0.595255944942072	0.5623492831620854	0.5707877144627533	0.5671885155689408	0.5703645398030198	0.6037160610378166	0.5908421577790883	0.5915830698702301

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	0.42008326880207764	0.3057450153908789	0.3099133524266701	0.42198502248674946

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	0.00930901537956004	0.008347750465763215	0.00557347082152631	0.009968981882333486

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