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 mr1864 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
vg1208780205 sf1208777612 12 8780205 1.58E-11 7.49E-07
vg0420503850 sf0420331894 4 20503850 1.86E-11 2.22E-06
vg1208278474 sf1208275880 12 8278474 4.66E-11 8.78E-07
vg0709448532 sf0709447538 7 9448532 5.68E-11 2.13E-06
vg0417424147 sf0417252190 4 17424147 1.00E-10 1.81E-06
vg0621838550 sf0621837553 6 21838550 1.62E-10 1.56E-06
vg0418239478 sf0418067524 4 18239478 2.00E-10 1.50E-06
vg1016429377 sf1016358151 10 16429377 4.48E-09 4.09E-06
vg0420664918 sf0420492961 4 20664918 1.80E-08 4.89E-06
vg1115833983 sf1115370291 11 15833983 1.16E-07 7.17E-06
vg1226737055 sf1226703453 12 26737055 3.86E-06 1.13E-07
vg0825541883 sf0825539169 8 25541883 6.46E-06 1.97E-06
vg0418681664 sf0418509711 4 18681664 NA 1.40E-06
vg0419549428 sf0419377466 4 19549428 NA 7.08E-06