• 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)

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

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'

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

• 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, ...)

• 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