QC Report

	general
Report generated at	2021-10-26 14:00:37
Title	daf-8_OP790_L4larva_1_5
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	8162778	9549530	9222796
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	8113498	9508647	9194623
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.4	99.6	99.7
Paired Reads	8162778	9549530	9222796
Paired Reads (QC-failed)	0	0	0
Read1	4081389	4774765	4611398
Read1 (QC-failed)	0	0	0
Read2	4081389	4774765	4611398
Read2 (QC-failed)	0	0	0
Properly Paired Reads	8074012	9471162	9131178
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	98.9	99.2	99.0
With itself	8101664	9497238	9184784
With itself (QC-failed)	0	0	0
Singletons	11834	11409	9839
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	9783	6961	24941
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	3704390	4347023	4181324
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	539946	650785	687887
Paired Optical Duplicate Reads	61248	66701	83709
% Duplicate Reads	14.5758	14.9708	16.4514

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	6328888	7392476	6986874
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	6328888	7392476	6986874
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	6328888	7392476	6986874
Paired Reads (QC-failed)	0	0	0
Read1	3164444	3696238	3493437
Read1 (QC-failed)	0	0	0
Read2	3164444	3696238	3493437
Read2 (QC-failed)	0	0	0
Properly Paired Reads	6328888	7392476	6986874
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	6328888	7392476	6986874
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	3684253	4323851	4138393
Distinct Fragments	3151715	3681789	3462203
Positions with Two Read	417724	499124	513409
NRF = Distinct/Total	0.855456	0.851507	0.836606
PBC1 = OneRead/Distinct	0.850242	0.84613	0.829615
PBC2 = OneRead/TwoRead	6.415052	6.241481	5.594559

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	67707	240
N1	31354	62
N2	34051	77
Np	77359	282
N optimal	77359	282
N conservative	67707	240
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.142555422629861	1.175
Self Consistency Ratio	1.0860177329846272	1.2419354838709677
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	99014	131444

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	81.0	85.0	81.0	81.0
25 percentile	324.0	300.0	324.0	324.0
50 percentile (median)	324.0	300.0	324.0	324.0
75 percentile	324.0	300.0	324.0	324.0
Max size	324.0	300.0	324.0	324.0
Mean	323.9975458016038	299.9983643224491	323.13829787234044	323.99685880117374

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	3465952	4061201
Estimated Fragment Length	220	185
Cross-correlation at Estimated Fragment Length	0.510403684213415	0.547287568143803
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.5110783	0.5479966
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.5069149	0.5444114
NSC (Normalized Strand Cross-correlation coeff.)	1.006882	1.005283
RSC (Relative Strand Cross-correlation coeff.)	0.8379628	0.8022274

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	0.4045193437826104	0.4096085471201171
Synthetic AUC	0.49747188893812067	0.4976600371328821
X-intercept	0.019550141254209695	0.01946235615213956
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5142191914194053	0.5069310328316282
Synthetic Elbow Point	0.5026835673981045	0.5010448002975486
JS Distance	0.033348996112551724	0.028959624482611506
Synthetic JS Distance	0.1379926972077194	0.13198144415426372
% Genome Enriched	45.55647774248639	45.268183486824256
Diff. Enrichment	10.533024286134934	9.7379152172688
CHANCE Divergence	0.08973956875403384	0.08288965196559689

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	0.5013972438760174	0.5850756904723127	0.4481779421598233	0.4334728986607464	0.4467375627440397	0.4432644759347207	0.5866304545233259	0.5785872308321535	0.5789963738298903

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	0.3361423106332577	0.1884520629848403	0.18689773223477493	0.37526691952782537

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	0.0025748897850097117	0.0008756672578184351	0.0009745043473932144	0.002970550158132967

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