• 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.

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

NOTE1: For SE datasets, reads from replicates are randomly subsampled.
NOTE2: For PE datasets, the first end of each read-pair is selected and the reads are then randomly subsampled.

• 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