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Table 2 Summary of the results of the genome wide association analysis for sperm quality traits

From: A systems biology framework integrating GWAS and RNA-seq to shed light on the molecular basis of sperm quality in swine

SSC Interval #SNP Interval Mbp Top SNP Top SNP location bp Top SNP P-value Top SNP FDR Top SNP MAF Beta Trait
1 I1 1 rs339761632 13,501,755 4.64 × 10–8 0.02 0.06 4.84 PDROP
1 I2 8 82.90–83.49 rs81354986 82,895,619 1.69 × 10–6 0.03 0.07 5.05 HABN
1 I3 8 94.88–98.74 rs327733412 94,880,167 1.61 × 10–7 0.02 0.07 5.65 HABN
1 I4 1 rs337166779 126,397,198 2.05 × 10–6 0.03 0.06 5.02 HABN
1 I5 11 243.86–246.44 rs343194423 246,224,386 1.72 × 10–7 0.01 0.07 3.17 NABN
1 I6 2 258.54–258.55 rs332256425 258,548,786 1.76 × 10–6 0.04 0.06 3.44 NABN
3 I1 1 rs332055717 2,911,413 6.35 × 10–8 0.01 0.09 5.07 HABN
3 I2 3 113.75–113.84 rs328292697 113,750,595 1.09 × 10–7 0.01 0.07 3.41 NABN
4 I1 2 2.41–2.42 rs318575212 2,412,006 2.88 × 10–8 0.01 0.08 4.11 ACRO_5
rs332927981 2,415,239
6 I1 2 65.60–66.66 rs335394654 65,597,553 1.86 × 10–7 0.03 0.14 3.04 ACRO_5
7 I1 2 6.20–6.38 rs326239534 6,377,172 9.87 × 10–6 0.02 0.17 -9.15 MT_5
7 I2 2 85.73–86.88 rs336588919 86,884,279 4.13 × 10–8 0.01 0.06 3.75 NABN
9 I1 2 5.76–5.78 rs1110111787 5,776,597 1.55 × 10–7 0.02 0.07 5.43 HABN
9 I2 1 rs342738178 28,463,580 1.53 × 10–5 0.03 0.14 − 10.42 MT_5, MT_90
9 I3 1 rs328217450 137,959,590 4.77 × 10–8 0.02 0.18 2.36 R_ACRO
13 I1 18 25.36–28.47 rs690794887 25,535,100 3.06 × 10–7 0.02 0.14 3.78 HABN
13 I2 3 33.82–37.65 rs327865244 33,819,549 3.79 × 10–8 0.01 0.15 4.28 HABN
16 I1 1 rs324239602 6,476,358 6.08 × 10–6 0.01 0.46 9.07 MT_90
  1. SSC, Sus scrofa chromosome; #SNP, number of SNPs significantly associated (FDR) with the trait; Interval, region of the GWAS interval; Beta, additive effect; FDR, false discovery rate; MAF, minor allele frequency; ACRO_5, abnormal acrosomes 5 min; HABN, head abnormalities; NABN, neck abnormalities; PDROP, proximal droplets; R_ACRO, ratio acrosomes; MT_5, motility 5 min; MT_90, motility 90 min