QC Report

	general
Report generated at	2021-09-14 02:44:56
Title	T22C8.4_OP785_midembryonic_1_6
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}}
Peak caller	spp

Alignment quality metrics

SAMstat (raw unfiltered BAM)

	rep1	rep2	ctl1
Total Reads	17780932	18128884	18317180
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17718092	18078722	18277992
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.6	99.7	99.8
Paired Reads	17780932	18128884	18317180
Paired Reads (QC-failed)	0	0	0
Read1	8890466	9064442	9158590
Read1 (QC-failed)	0	0	0
Read2	8890466	9064442	9158590
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17606200	17978146	18152900
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.0	99.2	99.1
With itself	17700188	18062046	18257010
With itself (QC-failed)	0	0	0
Singletons	17904	16676	20982
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5633	6279	10089
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	8010699	8170682	8361718
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	940233	888159	815257
Paired Optical Duplicate Reads	93823	88627	92702
% Duplicate Reads	11.7372	10.8701	9.7499

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	14140932	14565046	15092922
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	14140932	14565046	15092922
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	14140932	14565046	15092922
Paired Reads (QC-failed)	0	0	0
Read1	7070466	7282523	7546461
Read1 (QC-failed)	0	0	0
Read2	7070466	7282523	7546461
Read2 (QC-failed)	0	0	0
Properly Paired Reads	14140932	14565046	15092922
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	14140932	14565046	15092922
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	7972822	8131568	8310213
Distinct Fragments	7047420	7253619	7504245
Positions with Two Read	761031	733497	692668
NRF = Distinct/Total	0.88393	0.892032	0.903015
PBC1 = OneRead/Distinct	0.880977	0.889439	0.900461
PBC2 = OneRead/TwoRead	8.158164	8.795748	9.75544

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	39896	2326
N1	29929	1629
N2	29405	1319
Np	38468	2415
N optimal	39896	2415
N conservative	39896	2326
Optimal Set	rep1_vs_rep2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0371217635437247	1.0382631126397248
Self Consistency Ratio	1.0178200986226833	1.2350265352539802
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	74996	74009

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	66.0	66.0	72.0	72.0
25 percentile	264.0	264.0	290.0	290.0
50 percentile (median)	264.0	264.0	290.0	290.0
75 percentile	264.0	264.0	290.0	290.0
Max size	1299.0	1298.0	1841.0	1841.0
Mean	263.6405541628887	263.73387020497506	274.88115942028986	289.0587778223381

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	7509555	7654799
Estimated Fragment Length	145	140
Cross-correlation at Estimated Fragment Length	0.706134640558311	0.712579240486309
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7054991	0.712308
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6983509	0.7057774
NSC (Normalized Strand Cross-correlation coeff.)	1.011146	1.009637
RSC (Relative Strand Cross-correlation coeff.)	1.088906	1.04154

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	0.40659115473462903	0.4102286711410408
Synthetic AUC	0.4982960621101191	0.49831969002423354
X-intercept	0.019050166369589994	0.01895036457595216
Synthetic X-intercept	0.0	0.0
Elbow Point	0.538941661859547	0.5294724676791891
Synthetic Elbow Point	0.49827345289038555	0.5012137357401231
JS Distance	0.05578254099530593	0.04809778532753977
Synthetic JS Distance	0.14365700896372982	0.13810889755627972
% Genome Enriched	40.648072927166645	41.78820861768528
Diff. Enrichment	9.093983876292032	8.567598270092457
CHANCE Divergence	0.07732931141880993	0.0728169799568984

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	0.3530239025263681	0.3449303901958154	0.3542390275266156	0.34992744273825943	0.3535341234934161	0.34962009040274783	0.5080670304979681	0.3376713841506195	0.3437835383127193

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	0.20706206212517825	0.1638046205158189	0.15668381685852553	0.20123317171078442

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	0.026030327202229444	0.0214568601277483	0.017085081639975595	0.026622015804512913

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