added comment on individual masking

README.md

@@ -12,7 +12,11 @@ For mapping details please look into the original publication ([Harr et al. 2016
 
 For masking genomic regions in natural populations which showed low coverage based on the genomic mapping BAM files we only considered the stable chromosomes from the reference GRCm38 _mm10_ <http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/>.
 
-The BAM files were processed with 'genomeCoverageBed' to obtain site specific genome coverage and further united with 'unionBedGraphs'. The per population combined coverage was further processed to only retain regions with a coverage smaller than 5 resulting as the masking regions.
+The BAM files were processed with 'genomeCoverageBed' to obtain site specific genome coverage and further united with 'unionBedGraphs'.
+
+##### Population specific masking
+
+The per population combined coverage was further processed to only retain regions with a coverage smaller than 5 resulting as the masking regions.
 
 genomeCoverageBed example for the population _Mus musculus musculus AFG_:
 ```
@@ -56,6 +60,10 @@ bedtools merge -i $INPUT".stcov5" > $INPUT".stcov5.merge"
 awk -v OFS='\t' '{print $1,$2,$3,4}' $INPUT".stcov5.merge" > $OUTPUT
 ```
 
+##### Individual specific masking
+
+For individuals regions with a coverage smaller than 5 were used as masking regions.
+
 get masking region example for individual 396 of the population _Mus musculus musculus AFG_:
 ```
 INPUT=AFG1_396.bam.bga