Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1707 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0918158744 sf0918157743 9 18158744 5.61E-34 2.26E-24
vg0916150346 sf0916149345 9 16150346 3.62E-18 5.10E-07
vg0916915306 sf0916914305 9 16915306 1.57E-13 NA
vg0919214450 sf0919214040 9 19214450 5.39E-13 1.49E-06
vg0333724728 sf0333717598 3 33724728 9.69E-13 NA
vg0717420887 sf0717419894 7 17420887 2.02E-12 2.68E-08
vg0112995841 sf0112994815 1 12995841 3.43E-12 3.20E-08
vg0819068671 sf0819065958 8 19068671 7.03E-11 3.89E-06
vg1208919948 sf1208917356 12 8919948 1.70E-10 2.14E-06
vg0433383265 sf0433198154 4 33383265 6.89E-10 5.55E-07
vg1014079049 sf1014007815 10 14079049 1.06E-09 8.67E-07
vg1018711549 sf1018640106 10 18711549 2.79E-09 1.95E-06
vg1208920255 sf1208917663 12 8920255 3.53E-09 NA
vg1004778450 sf1004794987 10 4778450 4.40E-09 NA
vg1223180692 sf1223147152 12 23180692 5.20E-09 2.13E-06
vg0333663063 sf0333655933 3 33663063 1.97E-08 6.39E-07
vg0114877604 sf0114876578 1 14877604 3.70E-08 9.66E-07
vg0433351030 sf0433165920 4 33351030 6.45E-08 2.02E-06
vg0412820231 sf0412810941 4 12820231 NA 9.22E-09
vg0916208687 sf0916207686 9 16208687 NA 4.59E-08
vg1205898444 sf1205897425 12 5898444 NA 4.71E-08
vg0918198007 sf0918197006 9 18198007 NA 9.11E-08
vg0116741597 sf0116740571 1 16741597 NA 1.39E-07
vg0704750780 sf0704749781 7 4750780 NA 3.84E-07
vg0219817547 sf0219811679 2 19817547 NA 3.98E-07
vg1223317526 sf1223283986 12 23317526 NA 9.66E-07
vg0607377849 sf0607376850 6 7377849 NA 1.68E-06
vg1014042350 sf1013971116 10 14042350 NA 2.53E-06
vg0921003726 sf0921003245 9 21003726 NA 2.96E-06
vg0618287415 sf0618286418 6 18287415 NA 2.96E-06
vg1123105257 sf1122639128 11 23105257 NA 4.02E-06