The following zip contains the allele counts used for computing the allele frequency difference between the library preparation protocols. All files are in the .sync format created by PoPoolation2 https://sourceforge.net/p/popoolation2/wiki/Manual/ A sync file contains allele counts (A, T, C, G) for an arbitrary number of samples/populations. The order of populations in the file is the following: 91-r1 91-r2 92-r1 92-r2 93-r1 93-r2 105-r1 105-r2 where r1 is replicate 1 and r2 replicate 2 91: NEBNext Ultra (+); 92: NEXTflex (-); 93: NEBNext DNA (+); 105: TruSeq (-) The folder-structure of the file is the following: --Dmel--|--unmodified (unmodified reads; subsampled to counts of 30,40,50) |--trim_length50 (trimmed reads to length 50; subsampled to coverages 30,40) |--mergedset.. (merged sync file containing the unmodified and the trimmed data) --Dsim--|--unmodified |--trim_length50 |--mergedset.. Dsim: D.simulans; Dmel: D.melanogaster Note: sync files in the mergedset folder contain 16 samples/populations; the first 8 refer to the unmodified reads and the last 8 to the trimmed reads (length 50)