##This folder contains the SNP variants: 
(1) Main_JointGenotyping_filtered_snps_PASS_Nomissing_Biallelic_Linear_Chr.recode.vcf.gz: called from Illumina RNA-Seq data of 48 mice individuals reared under lab condition; The SNP data called from the Genomic sequencing dataset (same populations, but different individuals) can be found: https://wwwuser.gwdg.de/~evolbio/evolgen/wildmouse/mouse_retroCNV/

#### The filtered SNP datasets with Filters applied: 
#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;


##The Relation between the individual IDs here and those in the main text
CB_1  	       GE1
CB_3	       GE2
CB_5	       GE3
CB_7	       GE4
CB_9	       GE5
CB_11	       GE6
CB_13	       GE7
CB_15	       GE8
MC_1	       FR1
MC_3	       FR2
MC_5	       FR3
MC_8	       FR4
MC_9	       FR5
MC_11	       FR6
MC_13	       FR7
MC_16	       FR8
AH_1	       IR1
AH_3	       IR2
AH_5	       IR3
AH_7	       IR4
AH_9	       IR5
AH_11	       IR6
AH_13	       IR7
AH_15	       IR8
KH_1	       KA1
KH_3	       KA2
KH_5	       KA3
KH_7	       KA4
KH_9	       KA5
KH_11	       KA6
KH_13	       KA7
KH_15	       KA8
TW_1	       TA1
TW_3	       TA2
TW_5	       TA3
TW_7	       TA4
TW_9	       TA5
TW_11	       TA6
TW_13	       TA7
TW_15	       TA8
SC_1	       SL1
SC_5	       SL2
SC_7	       SL3
SC_10	       SL4
SP_1	       SP1
SP_3	       SP2
SP_9	       SP3
SP_11	       SP4