QC Report

	general
Report generated at	2021-09-01 04:43:18
Title	tra-1_DZ840_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	21973606	20826034	24759408
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	21895847	20750014	24653620
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.6	99.6
Paired Reads	21973606	20826034	24759408
Paired Reads (QC-failed)	0	0	0
Read1	10986803	10413017	12379704
Read1 (QC-failed)	0	0	0
Read2	10986803	10413017	12379704
Read2 (QC-failed)	0	0	0
Properly Paired Reads	21792116	20670730	24536678
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.3	99.1
With itself	21873302	20732634	24630256
With itself (QC-failed)	0	0	0
Singletons	22545	17380	23364
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	6040	6815	21978
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10019865	9468375	11292017
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1764341	1680839	2064467
Paired Optical Duplicate Reads	162713	144313	214656
% Duplicate Reads	17.6084	17.752100000000002	18.2825

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	16511048	15575072	18455100
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	16511048	15575072	18455100
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	16511048	15575072	18455100
Paired Reads (QC-failed)	0	0	0
Read1	8255524	7787536	9227550
Read1 (QC-failed)	0	0	0
Read2	8255524	7787536	9227550
Read2 (QC-failed)	0	0	0
Properly Paired Reads	16511048	15575072	18455100
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	16511048	15575072	18455100
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	9932223	9407939	11108345
Distinct Fragments	8195997	7749064	9092350
Positions with Two Read	1258691	1187813	1457763
NRF = Distinct/Total	0.825193	0.823673	0.818515
PBC1 = OneRead/Distinct	0.819532	0.818759	0.811215
PBC2 = OneRead/TwoRead	5.336404	5.341427	5.059707

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	55620	2703
N1	29821	1682
N2	38945	1355
Np	75095	3168
N optimal	75095	3168
N conservative	55620	2703
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.3501438331535418	1.172031076581576
Self Consistency Ratio	1.3059588880319237	1.241328413284133
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	77748	123890

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	70.0	68.0	76.0	76.0
25 percentile	280.0	270.0	304.0	304.0
50 percentile (median)	280.0	270.0	304.0	304.0
75 percentile	280.0	270.0	304.0	304.0
Max size	403.0	307.0	515.0	515.0
Mean	279.7029634202809	269.9080232464283	292.2929292929293	303.496144883148

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9390791	8861744
Estimated Fragment Length	155	130
Cross-correlation at Estimated Fragment Length	0.728272297353722	0.714805809107293
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7276565	0.7146908
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7220956	0.7094574
NSC (Normalized Strand Cross-correlation coeff.)	1.008554	1.007539
RSC (Relative Strand Cross-correlation coeff.)	1.110731	1.021981

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	0.40724363368203453	0.4101884736622618
Synthetic AUC	0.4984284310215867	0.4983755563064248
X-intercept	0.01865589702024699	0.018785659813860264
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5599843486107395	0.5383738525974519
Synthetic Elbow Point	0.49903890946650764	0.5016837985890372
JS Distance	0.06345634932691147	0.0625963634189198
Synthetic JS Distance	0.14710168903425994	0.13844970698780018
% Genome Enriched	40.966912483979286	44.03570273539969
Diff. Enrichment	8.613794852096385	8.560841878788516
CHANCE Divergence	0.07322504190831843	0.0727934927766989

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	0.37100721892395927	0.5196005514452838	0.3524793822899673	0.41044073504122486	0.3509842621740304	0.41024221268447425	0.49423411119823774	0.5153636525700209	0.5153349174035378

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	0.2789850876329079	0.16704275827918375	0.20066186531914587	0.354825482171107

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	0.027021029653943825	0.01987354164314706	0.014808663484830118	0.03059073518393623

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