QC Report

	general
Report generated at	2022-05-09 11:42:13
Title	isw-1_OP181_L1larva_2_7
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}, 'ctl2': {'paired_end': True}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1	ctl2
Total Reads	23504806	15135028	18563298	10736886
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	23394919	14840945	18073990	9750126
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	99.5	98.1	97.39999999999999	90.8
Paired Reads	23504806	15135028	18563298	10736886
Paired Reads (QC-failed)	0	0	0	0
Read1	11752403	7567514	9281649	5368443
Read1 (QC-failed)	0	0	0	0
Read2	11752403	7567514	9281649	5368443
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	23308660	14766660	17972678	9669420
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	99.2	97.6	96.8	90.10000000000001
With itself	23379772	14816804	18061076	9732266
With itself (QC-failed)	0	0	0	0
Singletons	15147	24141	12914	17860
Singletons (QC-failed)	0	0	0	0
% Singleton	0.1	0.2	0.1	0.2
Diff. Chroms	9854	5795	18813	6600
Diff. Chroms (QC-failed)	0	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1	ctl2
Unpaired Reads	0	0	0	0
Paired Reads	10778331	6811223	8284728	4450698
Unmapped Reads	0	0	0	0
Unpaired Duplicate Reads	0	0	0	0
Paired Duplicate Reads	1318898	875389	1153219	453575
Paired Optical Duplicate Reads	133419	110748	122293	57723
% Duplicate Reads	12.236600000000001	12.8522	13.919799999999999	10.1911

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	ctl2
Total Reads	18918866	11871668	14263018	7994246
Total Reads (QC-failed)	0	0	0	0
Duplicate Reads	0	0	0	0
Duplicate Reads (QC-failed)	0	0	0	0
Mapped Reads	18918866	11871668	14263018	7994246
Mapped Reads (QC-failed)	0	0	0	0
% Mapped Reads	100.0	100.0	100.0	100.0
Paired Reads	18918866	11871668	14263018	7994246
Paired Reads (QC-failed)	0	0	0	0
Read1	9459433	5935834	7131509	3997123
Read1 (QC-failed)	0	0	0	0
Read2	9459433	5935834	7131509	3997123
Read2 (QC-failed)	0	0	0	0
Properly Paired Reads	18918866	11871668	14263018	7994246
Properly Paired Reads (QC-failed)	0	0	0	0
% Properly Paired Reads	100.0	100.0	100.0	100.0
With itself	18918866	11871668	14263018	7994246
With itself (QC-failed)	0	0	0	0
Singletons	0	0	0	0
Singletons (QC-failed)	0	0	0	0
% Singleton	0.0	0.0	0.0	0.0
Diff. Chroms	0	0	0	0
Diff. Chroms (QC-failed)	0	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	ctl2
Total Fragments	10768014	6805114	8180559	4399155
Distinct Fragments	9452890	5938698	7046441	3955491
Positions with Two Read	1080399	701950	908112	376573
NRF = Distinct/Total	0.877868	0.872682	0.861364	0.899148
PBC1 = OneRead/Distinct	0.8739	0.868627	0.855911	0.896676
PBC2 = OneRead/TwoRead	7.646138	7.348831	6.641387	9.418612

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	10851	2143
N1	16052	2090
N2	24623	1756
Np	10442	2210
N optimal	10851	2210
N conservative	10851	2143
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0391687416203792	1.031264582361176
Self Consistency Ratio	1.5339521554946425	1.1902050113895217
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	29197	51623

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	90.0	72.0	94.0	94.0
25 percentile	360.0	290.0	219.0	376.0
50 percentile (median)	360.0	290.0	376.0	376.0
75 percentile	360.0	290.0	376.0	376.0
Max size	554.0	318.0	573.0	573.0
Mean	355.7662431071685	288.68012320089883	304.26651583710407	361.3644825361718

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	10185158	6422620
Estimated Fragment Length	175	160
Cross-correlation at Estimated Fragment Length	0.761452768103064	0.667432820939123
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7569461	0.6625811
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7484828	0.6553542
NSC (Normalized Strand Cross-correlation coeff.)	1.017328	1.018431
RSC (Relative Strand Cross-correlation coeff.)	1.532504	1.671353

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	0.41298406296807627	0.4101570293959189
Synthetic AUC	0.4985388225764624	0.4981528346257207
X-intercept	0.018338640924019926	0.018933623503808488
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5675235347555679	0.5462738716794282
Synthetic Elbow Point	0.500230722648011	0.49985285710375726
JS Distance	0.07691171227652926	0.07369192912256269
Synthetic JS Distance	0.14079342621332566	0.13993152482190335
% Genome Enriched	41.913527867346836	44.18664084415649
Diff. Enrichment	4.881997159036866	6.131795802051332
CHANCE Divergence	0.0414762894783973	0.052181190534840126

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	0.19496723535120974	0.2772896782490885	0.29585871628260213	0.390120747985877	0.2985860038953713	0.38321607376486605	0.12007476063909772	0.22104603830215883	0.21367139742827437

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	0.09318058595541084	0.12355159130573683	0.15074772980511247	0.0909995909781883

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	0.037018032879845474	0.03708002371812349	0.030412322851346586	0.03778511928373831

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