##general header##
This ftp site provides access to 'introgression' data for wild mouse species generated at the Max-Planck Institute for Evolutionary Biology in Plön ( http://www.evolbio.mpg.de/ ), Department of Evolutionary Genetics (Diethard Tautz).

##specific information for directory /introgression ##
The files are organized in sub-directories according to the data source. For example, all data associated with NextGenMap mapping are in the directory 'ngm', all data associated with simulations are in the directory 'simulations'.

Contents of further sub-directories within 'ngm' data sources are:

bam: 'bam' files generated with 'ngm --sensitive' mapped against 'mm10' and further sorting, marking and removing duplicates with 'picard-tools'
dK80: 'dK80' analysis files in tsv or bigWig format 
fasta: FASTA files generated with 'ANGSD' as chromosome alignments in sub-directories for each chromosome for either the CONSENSUS FASTA ('pop') or INDIVIDUAL FASTA ('ind'); the name indicates which 'ANGSD' filters were used
twisst: phylogenetic trees per 25kbp window as tsv files generated with 'distIUPAC' and 'ape' using the INDIVIDUAL FASTA files

Contents of further sub-directories within 'simulations' data sources are:

bam: 'bam' files generated with 'ngm --sensitive' mapped against simulated reference and further sorting, marking and removing duplicates with 'picard-tools'
dK80: 'dK80' analysis files in tsv or bigWig format
fasta: FASTA files generated with 'ANGSD' as chromosome alignments

A detailed protocol how the data was generated can be found here:

https://gitlab.gwdg.de/evolgen/introgression

Populations are abbreviated as follows:

FRA = Mus musculus domesticus FRA
GER = Mus musculus domesticus GER
IRA = Mus musculus domesticus IRA
AFG = Mus musculus musculus AFG
CAS = Mus musculus castaneus CAS
SPRE = Mus spretus