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 mr1155 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
vg0719051105 sf0719050112 7 19051105 5.69E-53 1.21E-37
vg0719209499 sf0719208506 7 19209499 5.90E-31 1.25E-23
vg0719140026 sf0719139033 7 19140026 2.18E-15 2.45E-06
vg0719153233 sf0719152240 7 19153233 6.14E-15 3.19E-06
vg0719255309 sf0719254316 7 19255309 1.82E-14 8.64E-09
vg0725365363 sf0725364369 7 25365363 1.26E-13 2.10E-08
vg0719144612 sf0719143619 7 19144612 1.34E-13 4.89E-08
vg0719146275 sf0719145282 7 19146275 6.12E-13 1.08E-08
vg0719005656 sf0719004663 7 19005656 4.23E-12 1.29E-06
vg0718985954 sf0718984961 7 18985954 9.29E-12 1.12E-10
vg0504540636 sf0504540613 5 4540636 2.32E-10 1.30E-06
vg0717854157 sf0717853164 7 17854157 2.39E-10 1.79E-06
vg0335766999 sf0335759868 3 35766999 2.79E-08 2.18E-07
vg0715893635 sf0715892642 7 15893635 4.45E-08 1.28E-07
vg0430485059 sf0430299937 4 30485059 4.97E-08 NA
vg0336405494 sf0336398364 3 36405494 NA 1.29E-07
vg0335510866 sf0335503735 3 35510866 NA 5.64E-07
vg0139286980 sf0139285937 1 39286980 NA 6.38E-07
vg0402536732 sf0402532337 4 2536732 NA 1.57E-06
vg0412688323 sf0412679034 4 12688323 NA 3.50E-06
vg1109858246 sf1109852823 11 9858246 NA 4.15E-06
vg0915970058 sf0915969057 9 15970058 NA 4.18E-06