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Files	Path
Alignment
Replicate 1
Filtered & deduped bam	./align/rep1/SRR1370875_1.nodup.bam
Fastq
Bam	./align/rep1/SRR1370875_1.bam
Tag-align	./align/rep1/SRR1370875_1.nodup.tagAlign.gz
Control 1
Filtered & deduped bam	./align/ctl1/ss_50M_2000_GRCh38.nodup.bam
Bam
Tag-align	./align/ctl1/ss_50M_2000_GRCh38.nodup.tagAlign.gz
Pseudo-replicates
Replicate 1
Pseudo-replicate 1
Tag-align	./align/pseudo_reps/rep1/pr1/SRR1370875_1.nodup.pr1.tagAlign.gz
Pseudo-replicate 2
Tag-align	./align/pseudo_reps/rep1/pr2/SRR1370875_1.nodup.pr2.tagAlign.gz
QC and logs
Replicate 1
BWA map. flagstat log	./qc/rep1/SRR1370875_1.flagstat.qc
Dedup. log	./qc/rep1/SRR1370875_1.dup.qc
PBC log	./qc/rep1/SRR1370875_1.nodup.pbc.qc
Cross-corr. log	./qc/rep1/SRR1370875_1.nodup.15M.cc.qc
Cross-corr. plot	./qc/rep1/SRR1370875_1.nodup.15M.cc.plot.pdf
Control 1
Dedup. log	./qc/ctl1/ss_50M_2000_GRCh38.dup.qc
PBC log	./qc/ctl1/ss_50M_2000_GRCh38.nodup.pbc.qc

Flagstat QC (all)

	Reads (QC-passed)	Reads (QC-failed)	Dupes (QC-passed)	Dupes (QC-failed)	Mapped Reads	% Mapped
rep1	18838325	0	0	0	18563460	98.54

Dup QC (all)

	Unpaired Reads	Paired Reads	Unmapped Reads	Unpaired Dupes	Paired Dupes	Paired Opt. Dupes	% Dupes
rep1	16143944	0	0	728601	0	0	0.045132
ctl1	0	49994743	0	0	248112	42648	0.004963

Flagstat QC (all, filtered)

	Reads (QC-passed)	Reads (QC-failed)	Dupes (QC-passed)	Dupes (QC-failed)	Mapped Reads	% Mapped
rep1	15415343	0	0	0	15415343	100.00
ctl1	99493262	0	0	0	99493262	100.00

PBC QC (all)

	Total Read Pairs	Distinct Read Pairs	One Read Pair	Two Read Pairs	NRF = Distinct/Total	PBC1 = OnePair/Distinct	PBC2 = OnePair/TwoPair
rep1	16139160	15456588	14812661	611491	0.957707	0.958340	24.223841
ctl1	97578156	96132111	94755797	1345982	0.985181	0.985683	70.399008

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

Cross-correlation QC (all)

	numReads	estFragLen	corr_estFragLen	PhantomPeak	corr_phantomPeak	argmin_corr	min_corr	NSC	RSC
rep1	15000000	145	0.202636458767964	75	0.1937873	1500	0.173343	1.168991	1.432843

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
Important columns highlighted, but all/whole file can be stored for display