QC Report

	general
Report generated at	2021-09-01 17:45:30
Title	ztf-25_RW12287_youngadult_1_3
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	22526282	17758182	17681366
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	22414781	17667171	17644104
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	99.5	99.5	99.8
Paired Reads	22526282	17758182	17681366
Paired Reads (QC-failed)	0	0	0
Read1	11263141	8879091	8840683
Read1 (QC-failed)	0	0	0
Read2	11263141	8879091	8840683
Read2 (QC-failed)	0	0	0
Properly Paired Reads	22354250	17610698	17537478
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	99.2	99.2	99.2
With itself	22401830	17653240	17633042
With itself (QC-failed)	0	0	0
Singletons	12951	13931	11062
Singletons (QC-failed)	0	0	0
% Singleton	0.1	0.1	0.1
Diff. Chroms	5506	6486	28236
Diff. Chroms (QC-failed)	0	0	0

Marking duplicates (filtered BAM)

	rep1	rep2	ctl1
Unpaired Reads	0	0	0
Paired Reads	10175842	8034470	7978312
Unmapped Reads	0	0	0
Unpaired Duplicate Reads	0	0	0
Paired Duplicate Reads	1432875	1187588	909579
Paired Optical Duplicate Reads	88736	114448	59637
% Duplicate Reads	14.0811	14.7812	11.400599999999999

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	17485934	13693764	14137466
Total Reads (QC-failed)	0	0	0
Duplicate Reads	0	0	0
Duplicate Reads (QC-failed)	0	0	0
Mapped Reads	17485934	13693764	14137466
Mapped Reads (QC-failed)	0	0	0
% Mapped Reads	100.0	100.0	100.0
Paired Reads	17485934	13693764	14137466
Paired Reads (QC-failed)	0	0	0
Read1	8742967	6846882	7068733
Read1 (QC-failed)	0	0	0
Read2	8742967	6846882	7068733
Read2 (QC-failed)	0	0	0
Properly Paired Reads	17485934	13693764	14137466
Properly Paired Reads (QC-failed)	0	0	0
% Properly Paired Reads	100.0	100.0	100.0
With itself	17485934	13693764	14137466
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	10125048	7997432	7916308
Distinct Fragments	8706036	6821055	7017744
Positions with Two Read	1114334	918457	745649
NRF = Distinct/Total	0.859851	0.852906	0.886492
PBC1 = OneRead/Distinct	0.855555	0.847554	0.88339
PBC2 = OneRead/TwoRead	6.684258	6.294485	8.314106

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	77329	1092
N1	39296	515
N2	37311	295
Np	88736	1368
N optimal	88736	1368
N conservative	77329	1092
Optimal Set	pooled-pr1_vs_pooled-pr2	pooled-pr1_vs_pooled-pr2
Conservative Set	rep1_vs_rep2	rep1_vs_rep2
Rescue Ratio	1.1475125761357317	1.2527472527472527
Self Consistency Ratio	1.0532014687357616	1.7457627118644068
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	139892	112807

Top 300000 raw peaks from spp with FDR 0.01

Peak calling statistics

Peak region size

	rep1	rep2	idr_opt	overlap_opt
Min size	64.0	66.0	69.0	69.0
25 percentile	256.0	260.0	276.0	276.0
50 percentile (median)	256.0	260.0	276.0	276.0
75 percentile	256.0	260.0	276.0	276.0
Max size	256.0	260.0	276.0	276.0
Mean	255.98047779715782	259.98354712030283	271.9576023391813	275.93746619185

Enrichment / Signal-to-noise ratio

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

	rep1	rep2
Number of Subsampled Reads	9499387	7505281
Estimated Fragment Length	150	165
Cross-correlation at Estimated Fragment Length	0.741293222960803	0.691847321135049
Phantom Peak	50	50
Cross-correlation at Phantom Peak	0.7413208	0.692059
Argmin of Cross-correlation	1500	1500
Minimum of Cross-correlation	0.7367929	0.68779
NSC (Normalized Strand Cross-correlation coeff.)	1.006108	1.005899
RSC (Relative Strand Cross-correlation coeff.)	0.9939094	0.9504095

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	0.4172801772828794	0.41452941807410365
Synthetic AUC	0.49846926842988093	0.4982751867460722
X-intercept	0.019156223926417106	0.01930792477234893
Synthetic X-intercept	0.0	0.0
Elbow Point	0.5029262294754744	0.5041338480516422
Synthetic Elbow Point	0.49932715761396723	0.49921168509376856
JS Distance	0.032159561844416144	0.035962096811660196
Synthetic JS Distance	0.12586649880405568	0.1275239735414899
% Genome Enriched	42.79600627562447	44.61222469290559
Diff. Enrichment	7.798332144177139	8.35870957509352
CHANCE Divergence	0.06626685909442334	0.07108592880873955

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	0.548830505708188	0.4784390179354632	0.38650581816152135	0.4027158639509196	0.3884196735981817	0.40619306715085784	0.5433464108600411	0.5491096450575214	0.550335833935007

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	0.3362117554826862	0.18400944439113176	0.1813565649298469	0.3779131856889698

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	0.008990690031699474	0.005025296332469287	0.0030512428869082305	0.010825505750568848

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