QC Report

	general
Report generated at	2021-08-28 16:29:06
Title	ceh-88_OP593_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	15580162	14617096	20996252
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	15529318	14552699	20773087
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.7	99.6	98.9
Paired Reads	15580162	14617096	20996252
Paired Reads (QC-failed)	0	0	0
Read1	7790081	7308548	10498126
Read1 (QC-failed)	0	0	0
Read2	7790081	7308548	10498126
Read2 (QC-failed)	0	0	0
Properly Paired Reads	15477444	14500750	20460028
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.3	99.2	97.39999999999999
With itself	15513912	14536832	20752874
With itself (QC-failed)	0	0	0
Singletons	15406	15867	20213
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5376	5901	33686
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	7169102	6709424	9448345
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1117147	1029427	1682518
Paired Optical Duplicate Reads	136240	122798	207905
% Duplicate Reads	15.582799999999999	15.343000000000002	17.8075

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	12103910	11359994	15531654
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	12103910	11359994	15531654
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	12103910	11359994	15531654
Paired Reads (QC-failed)	0	0	0
Read1	6051955	5679997	7765827
Read1 (QC-failed)	0	0	0
Read2	6051955	5679997	7765827
Read2 (QC-failed)	0	0	0
Properly Paired Reads	12103910	11359994	15531654
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	12103910	11359994	15531654
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	7098795	6641726	9163744
Distinct Fragments	6005499	5633503	7579441
Positions with Two Read	843554	782949	1176693
NRF = Distinct/Total	0.845989	0.848199	0.827112
PBC1 = OneRead/Distinct	0.839967	0.842171	0.819639
PBC2 = OneRead/TwoRead	5.979959	6.059622	5.27955

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	82971	1171
N1	49285	1128
N2	59380	698
Np	83420	1349
N optimal	83420	1349
N conservative	82971	1171
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.0054115293295247	1.15200683176772
Self Consistency Ratio	1.204829055493558	1.6160458452722064
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	128937	128109

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	88.0	90.0	100.0	100.0
25 percentile	350.0	360.0	396.0	396.0
50 percentile (median)	350.0	360.0	396.0	396.0
75 percentile	350.0	360.0	396.0	396.0
Max size	350.0	360.0	493.0	493.0
Mean	349.7960942165554	359.88981258147356	370.58710155670866	395.58990649724285

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	6711133	6274185
Estimated Fragment Length	185	190
Cross-correlation at Estimated Fragment Length	0.663861496477332	0.648781264173627
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.6616572	0.6476228
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.6552035	0.6423925
NSC (Normalized Strand Cross-correlation coeff.)	1.013214	1.009945
RSC (Relative Strand Cross-correlation coeff.)	1.34155	1.22149

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	0.3933180817790798	0.39699173143928174
Synthetic AUC	0.4981740864891995	0.4981153800674083
X-intercept	0.018739869531543184	0.01882969634544598
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5984701495516644	0.5826566380019322
Synthetic Elbow Point	0.5002337312243643	0.4984119801799139
JS Distance	0.05917289897101154	0.05490502488231392
Synthetic JS Distance	0.16759463884135725	0.16094127592981938
% Genome Enriched	51.26496115489336	53.81125190632461
Diff. Enrichment	4.15824914502248	3.8418482850411717
CHANCE Divergence	0.03655505571312154	0.03421776786467065

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	0.5889161436263158	0.5888825293393641	0.5102247934386833	0.5698162217662752	0.5162139368541135	0.5670496951054191	0.6021123339065826	0.5903724136661292	0.5901890137615656

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	0.42095045223505856	0.2795067048581822	0.3221856455205874	0.42404102914843156

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	0.020917917154792316	0.021589552466930107	0.01349243670375178	0.02331615403813449

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