QC Report

	general
Report generated at	2021-09-01 00:47:01
Title	snpc-1.2_RW12251_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	22912446	24919346	22427978
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	21998102	24117234	21663482
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	96.0	96.8	96.6
Paired Reads	22912446	24919346	22427978
Paired Reads (QC-failed)	0	0	0
Read1	11456223	12459673	11213989
Read1 (QC-failed)	0	0	0
Read2	11456223	12459673	11213989
Read2 (QC-failed)	0	0	0
Properly Paired Reads	21967578	24078582	21599328
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	95.89999999999999	96.6	96.3
With itself	21989500	24107094	21652326
With itself (QC-failed)	0	0	0
Singletons	8602	10140	11156
Singletons (QC-failed)	0	0	0
% Singleton	0.0	0.0	0.0
Diff. Chroms	3594	4094	22393
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10064829	11028982	9949357
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1370537	1536236	838087
Paired Optical Duplicate Reads	75821	88256	56276
% Duplicate Reads	13.617099999999999	13.9291	8.4235

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	17388584	18985492	18222540
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17388584	18985492	18222540
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17388584	18985492	18222540
Paired Reads (QC-failed)	0	0	0
Read1	8694292	9492746	9111270
Read1 (QC-failed)	0	0	0
Read2	8694292	9492746	9111270
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17388584	18985492	18222540
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	17388584	18985492	18222540
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	9922008	10869293	9808469
Distinct Fragments	8580421	9367041	8991959
Positions with Two Read	1056064	1184068	715813
NRF = Distinct/Total	0.864787	0.861789	0.916755
PBC1 = OneRead/Distinct	0.861306	0.857637	0.915036
PBC2 = OneRead/TwoRead	6.998033	6.784675	11.49458

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	62619	2766
N1	39417	1428
N2	44196	1755
Np	63217	2842
N optimal	63217	2842
N conservative	62619	2766
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0095498171481498	1.027476500361533
Self Consistency Ratio	1.121242103660857	1.2289915966386555
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	101571	100937

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	78.0	79.0	85.0	85.0
25 percentile	310.0	316.0	340.0	340.0
50 percentile (median)	310.0	316.0	340.0	340.0
75 percentile	310.0	316.0	340.0	340.0
Max size	682.0	975.0	986.0	986.0
Mean	309.66246271081314	315.61242160951883	318.1446164672766	338.97949918534573

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9319035	10209563
Estimated Fragment Length	155	150
Cross-correlation at Estimated Fragment Length	0.742129531200228	0.757271306211439
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7413712	0.756775
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7339445	0.7497185
NSC (Normalized Strand Cross-correlation coeff.)	1.011152	1.010074
RSC (Relative Strand Cross-correlation coeff.)	1.102107	1.070332

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	0.3928154030415672	0.39619304835237656
Synthetic AUC	0.4984630858153457	0.49852987634282114
X-intercept	0.019012386101372774	0.018906573178620198
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5514789851542473	0.5622120091677913
Synthetic Elbow Point	0.4989848169274419	0.49985569932858304
JS Distance	0.05744004799771887	0.057737647539479506
Synthetic JS Distance	0.1709022980849854	0.1677953574016936
% Genome Enriched	34.256035329537376	31.921163383138612
Diff. Enrichment	8.540078248234629	8.284697302665943
CHANCE Divergence	0.07314876206439937	0.07159252798653659

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	0.46225316564016944	0.4543216472873076	0.40148720562870444	0.43348489467641926	0.4228758362383044	0.41669628577442186	0.4305028394398252	0.4562763876118805	0.456590457445572

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	0.3197198741213385	0.22696833738733413	0.244685468251231	0.32174370559955945

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	0.03583002355853658	0.025848798269025242	0.02880920863151716	0.0362697873067621

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