QC Report

	general
Report generated at	2021-08-31 16:56:48
Title	nhr-19_OP791_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	41417246	38449830	38206300
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	40911821	38031863	36602951
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	98.8	98.9	95.8
Paired Reads	41417246	38449830	38206300
Paired Reads (QC-failed)	0	0	0
Read1	20708623	19224915	19103150
Read1 (QC-failed)	0	0	0
Read2	20708623	19224915	19103150
Read2 (QC-failed)	0	0	0
Properly Paired Reads	40728978	37876498	36242812
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.3	98.5	94.89999999999999
With itself	40888518	38011496	36573058
With itself (QC-failed)	0	0	0
Singletons	23303	20367	29893
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	10534	10215	130248
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	18882371	17544442	16756236
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	3079914	2731375	2251261
Paired Optical Duplicate Reads	123428	113818	91252
% Duplicate Reads	16.3111	15.568299999999999	13.4354

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	31604914	29626134	29009950
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	31604914	29626134	29009950
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	31604914	29626134	29009950
Paired Reads (QC-failed)	0	0	0
Read1	15802457	14813067	14504975
Read1 (QC-failed)	0	0	0
Read2	15802457	14813067	14504975
Read2 (QC-failed)	0	0	0
Properly Paired Reads	31604914	29626134	29009950
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	31604914	29626134	29009950
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	18601136	17360400	16068007
Distinct Fragments	15610107	14683180	14076272
Positions with Two Read	2248837	2050853	1611923
NRF = Distinct/Total	0.839202	0.845786	0.876043
PBC1 = OneRead/Distinct	0.833845	0.840416	0.872764
PBC2 = OneRead/TwoRead	5.788062	6.017	7.621494

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	18239	4560
N1	16926	3780
N2	22431	3763
Np	17831	4475
N optimal	18239	4560
N conservative	18239	4560
Optimal Set	rep1_vs_rep2	rep1_vs_rep2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0228814985138242	1.0189944134078213
Self Consistency Ratio	1.3252392768521801	1.0045176720701567
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	30567	45604

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	95.0	91.0	100.0	100.0
25 percentile	380.0	364.0	227.0	400.0
50 percentile (median)	380.0	364.0	400.0	400.0
75 percentile	380.0	364.0	400.0	400.0
Max size	1658.0	1005.0	2096.0	2096.0
Mean	371.12745771583735	358.6663450574511	328.1467105263158	381.793519381545

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	15000000	15000000
Estimated Fragment Length	160	150
Cross-correlation at Estimated Fragment Length	0.816927629629887	0.815475869519713
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.8092544	0.8082964
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7959642	0.7961069
NSC (Normalized Strand Cross-correlation coeff.)	1.026337	1.02433
RSC (Relative Strand Cross-correlation coeff.)	1.577356	1.58899

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	0.38516586761046745	0.38860200381280524
Synthetic AUC	0.4988673075122305	0.49882959588957604
X-intercept	0.01792422668052114	0.018056110622652066
Synthetic X-intercept	0.0	0.0
Elbow Point	0.6879925665414436	0.6694688673966909
Synthetic Elbow Point	0.49914312664876137	0.5017971444930905
JS Distance	0.09373336832590853	0.09734524233409296
Synthetic JS Distance	0.1956711890426927	0.18684150079758516
% Genome Enriched	29.18971305251379	34.84093997282392
Diff. Enrichment	5.035429674359504	4.616093328480375
CHANCE Divergence	0.04335481446003797	0.03927379344404097

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	0.22975822683776326	0.2917287486784472	0.2824350490284486	0.3269439524614347	0.28193066951111906	0.3275447500200161	0.24081459458280055	0.2479557594404878	0.2518156639628748

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	0.16394494832098905	0.1580453912957966	0.17934452736897769	0.16201426113105233

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	0.078165835084188	0.07119354920567099	0.06722520731189564	0.07744410972681702

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