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 mr1182 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
vg0919855604 sf0919855123 9 19855604 1.57E-20 2.23E-09
vg0724290261 sf0724289267 7 24290261 9.58E-20 8.99E-08
vg0819260710 sf0819257997 8 19260710 4.20E-19 1.25E-07
vg0819131363 sf0819128650 8 19131363 4.37E-19 1.23E-07
vg0132364610 sf0132363566 1 32364610 1.74E-18 1.54E-06
vg0604882288 sf0604881289 6 4882288 1.15E-17 3.56E-06
vg0821888365 sf0821885652 8 21888365 1.49E-17 1.04E-06
vg1214688591 sf1214685930 12 14688591 1.86E-17 5.22E-07
vg0604783076 sf0604782077 6 4783076 2.71E-17 3.52E-06
vg1203657863 sf1203656862 12 3657863 1.63E-16 1.25E-06
vg0803654150 sf0803653153 8 3654150 2.75E-16 1.09E-06
vg0134272325 sf0134271282 1 34272325 5.20E-16 3.28E-08
vg1208119667 sf1208117073 12 8119667 1.54E-15 4.00E-06
vg0137325195 sf0137324152 1 37325195 1.04E-14 3.09E-06
vg0223561709 sf0223555840 2 23561709 1.09E-14 1.54E-06
vg0812038921 sf0812037926 8 12038921 1.01E-13 4.18E-06
vg0917493665 sf0917492664 9 17493665 1.83E-12 9.44E-07
vg1104909930 sf1104905741 11 4909930 NA 5.22E-08
vg0803657241 sf0803656244 8 3657241 NA 2.25E-07
vg0619194263 sf0619193266 6 19194263 NA 4.66E-07
vg0618517700 sf0618516703 6 18517700 NA 9.99E-07
vg1219779242 sf1219750712 12 19779242 NA 1.13E-06
vg0814576026 sf0814573312 8 14576026 NA 4.40E-06