|
SSC
|
Interval
|
Top SNP of the GWAS interval
|
# SNPs called
|
Highest LD
|
SNP with highest LD
|
Genotypic frequency (0/0; 0/1; 1/1)
|
# called samples
|
SNP effect
|
Gene
|
Trait
|
|---|
|
1
|
I3
|
rs327733412
|
3
|
0.07
|
rs710447566
|
0.34; 0.54; 0.11
|
35
|
Low
|
KATNAL2
|
HABN
|
|
7
|
I2
|
rs336588919
|
2
|
0.4
|
rs330912302
|
0.63; 0.12; 0.25
|
32
|
Low
|
CHD2
|
NABN
|
|
13
|
I1
|
rs690794887
|
21
|
0.4
|
rs331304027
|
0.06; 0.09; 0.85
|
33
|
Moderate
|
ULK4
|
HABN
|
|
13
|
I2
|
rs327865244
|
11
|
0.2
|
rs323872641
|
0.49; 0.37; 0.14
|
35
|
Low
|
ABHD14A
|
HABN
|
- SSC, Sus scrofa chromosome; # SNPs called, number of SNPs identified in the SNP calling analysis; LD, linkage disequilibrium; Genotypic frequency: allelic frequency for each of the genotypes; # called samples, number of samples with reads in the given SNP position; HABN, head abnormalities; NABN, neck abnormalities
- The columns SNP effect and gene refer to the SNP with the highest LD in the region
