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 mr1512 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
vg0207908595 sf0207908594 2 7908595 7.64E-08 7.64E-08
vg0130122521 sf0130121476 1 30122521 7.88E-08 7.89E-08
vg0300249514 sf0300248514 3 249514 1.03E-07 1.03E-07
vg0820865298 sf0820862585 8 20865298 1.31E-07 1.31E-07
vg1104978992 sf1104974803 11 4978992 1.45E-07 1.45E-07
vg1215178307 sf1215175643 12 15178307 5.75E-07 5.75E-07
vg0709984451 sf0709983457 7 9984451 7.95E-07 7.95E-07
vg0125460621 sf0125459577 1 25460621 9.41E-07 9.42E-07
vg0822105767 sf0822103054 8 22105767 1.57E-06 1.57E-06
vg1104925598 sf1104921409 11 4925598 1.78E-06 1.78E-06
vg0431614108 sf0431429003 4 31614108 2.00E-06 2.00E-06
vg0820872709 sf0820869996 8 20872709 2.50E-06 2.50E-06
vg0119598439 sf0119597394 1 19598439 2.68E-06 2.68E-06
vg1207539985 sf1207537391 12 7539985 2.83E-06 2.83E-06
vg0129577181 sf0129576136 1 29577181 2.98E-06 2.98E-06
vg1210206055 sf1210203466 12 10206055 3.32E-06 3.32E-06
vg0431411704 sf0431226602 4 31411704 3.96E-06 3.96E-06