# --------------- #
# Datasets README #
# --------------- #

# ----- Recombination map
02_recombination_map_moving-median_Dmel_501k_version6.txt

# ----- Annnotated repeats
dmel6_XY234_MT_wMel_repeats_ge_200bp_sort.bed

# ----- FASTA ref
dmel6.03-clean.wMel_wRi_Lactobacillus_Acetobacter.fa

# ----- Empirical sync file (2L, 2R, 3L, 3R, 4, X)
#column labels: chr - pos - ref - F0 Sam - F0 Or - F20 R1 - F20 R2 - .... - F20 R10
empirical_parents_F20.sync
#           2L       2R       3L       3R       4        X #chr
#[1,] 23513712 25286936 28110227 32079331 1348131 23542271 #length in bp

# ----- Downsampled simulated neutral sync file (2L, 2R, 3L, 3R, X)
#column labels: chr - pos - ref - F20 R1 - F20 R2 - .... - F20 R10
neutral_F20.sync

# ----- 250bp-windows boundaries (2, 3, X)
#column labels: wsmooth (window size in number of SNPs) - unit (cM or bp) - chr - 
#pos_left - pos_right - pos_mean - nb_SNPs (matches wsmooth except for last windows) - size (in cM or bpå)
windows_boundaries.txt

# ----- Estimates per marker (s, Oregon-R AF, counts, markers, NA for 4)
count_freq_s_empirical_neutral.txt
#column labels: CHROM (arm) - POS (pos per arm) - CHROM_ALL (chromosome) - POS_ALL (pos per chromosome) - cM_fit (cM) - 
#cM_Mb (recombination rate) - REF (ref allele) - ALT (alternate allele) - QUAL (Freebayes QUAL score) - 
#sam_GT (Sam genotype) - sam_AO (Samarkand AO, #reads alternate allele) - sam_AO_RO (Samarkand AO+RO, #reads at the marker position in Samarkand) -
#or_GT (Oregon-R genotype) - or_AO (Oregon-R AO, #reads alternate allele) - or_AO_RO (Oregon-R AO+RO, #reads at the marker position in Oregon-R) -
#sam (identity of the Sam allele among ALT and REF) - or (identity of the Oregon-R allele among ALT and REF) -
#F20.R1.count.29 (total count in empirical R1 at F20) - ... - F20.R10.count.29 (total count in empirical R10 at F20) -
#F20.R1.freq.29 (Oregon-R AF in empirical R1 at F20) - ... - F20.R10.freq.29 (Oregon-R AF in empirical R10 at F20) -
#s_0_20.R1.29 (selection coeff. of Oregon-R allele in empirical R1 at F20) - ... - s_0_20.R1.29 (selection coeff. of Oregon-R allele in empirical R10 at F20) -
#F20.R1.cov.neutral (total count in neutral R1 at F20) - ... - F20.R10.cov.neutral (total count in neutral R10 at F20) -
#F20.R1.freq.neutral (Oregon-R AF in neutral R1 at F20) - ... - F20.R10.freq.neutral (Oregon-R AF in neutral R10 at F20) 

# ----- Smoothed allele frequency per 250bp-window 
smoothed_freq_empirical_neutral.txt
#column labels: CHROM_ALL (chromosome) - POS_ALL (pos per chromosome) - cM (cM) - 
#F20.R1.smoothed.freq.29 (smoothed Oregon-R AF in empirical R1 at F20) - ... -  F20.R10.smoothed.freq.29 (smoothed Oregon-R AF in empirical R10 at F20) -
#F20.R1.smoothed.freq.neutral (smoothed Oregon-R AF in neutral R1 at F20) - ... -  F20.R10.smoothed.freq.neutral (smoothed Oregon-R AF in neutral R10 at F20) 

# ----- 6targets_v2.txt
Mimics EE2input file containing the position of the 6 targets of selection on X

# ----- Scripts.zip
Contains annotated command lines and scripts for the project  (see internal README.txt file)
