See https://github.com/crazyhottommy/phantompeakqualtools for more details COL1: Filename: tagAlign/BAM filename COL2: numReads: effective sequencing depth i.e. total number of mapped reads in input file COL3: estFragLen: comma separated strand cross-correlation peak(s) in decreasing order of correlation. The top 3 local maxima locations that are within 90% of the maximum cross-correlation value are output. In almost all cases, the top (first) value in the list represents the predominant fragment length. If you want to keep only the top value simply run sed -r 's/,[^\t]+//g' <outFile> > <newOutFile> COL4: corr_estFragLen: comma separated strand cross-correlation value(s) in decreasing order (col2 follows the same order) COL5: phantomPeak: Read length/phantom peak strand shift COL6: corr_phantomPeak: Correlation value at phantom peak COL7: argmin_corr: strand shift at which cross-correlation is lowest COL8: min_corr: minimum value of cross-correlation COL9: Normalized strand cross-correlation coefficient (NSC) = COL4 / COL8 COL10: Relative strand cross-correlation coefficient (RSC) = (COL4 - COL8) / (COL6 - COL8) COL11: QualityTag: Quality tag based on thresholded RSC (codes: -2:veryLow,-1:Low,0:Medium,1:High,2:veryHigh)