##This folder contains the SNP variants called from house mouse population genomic dataset. For details, see our publication: Wenyu Zhang, Chen Xie, Kristian Ullrich, Yong E. Zhang and Diethard Tautz. The mutational load in natural populations is significantly affected by high primary rates of retroposition. Proc Natl Acad Sci USA. 2021 Feb 9;118(6):e2013043118. doi: 10.1073/pnas.2013043118.

#### 1) Mouse_Genomes.all.vcf.gz: The raw genetic variants called from GATK v3 pipeline.

#### 2) MouseGenomes.all.filtered_snps_PASS_Nomissing_Biallelic_Linear_Chr_Outgroup_Fixed.recode.vcf.gz: The filtered house mouse lineage-specific SNP datasets. 
##Filters applied including: 
#a) Hard filtering of low quality variants: "QD < 2.0 || FS > 60.0 || MQ < 40.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0 || SOR > 3.0";
#b) Only bi-allelic SNPs with non-missing values were included;
#c) Only SNPs locating in the linear complete chromosomes (1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 X Y) were included;
#d) Only house mouse lineage-specific SNPs (i.e., outgroup species (M.Spret, M.Splicilegus) have fixed allele (0/0 or 1/1), and in-group has alternative allele) were kept.