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 mr1817 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
vg1116233106 sf1115767976 11 16233106 7.57E-08 NA
vg0314232327 sf0314231016 3 14232327 9.82E-08 NA
vg0801689793 sf0801688795 8 1689793 1.34E-07 NA
vg0804583372 sf0804582375 8 4583372 2.62E-07 1.62E-07
vg1018126750 sf1018055521 10 18126750 4.15E-07 4.63E-06
vg0125184019 sf0125182975 1 25184019 5.27E-07 4.00E-06
vg1018126765 sf1018055536 10 18126765 8.54E-07 7.16E-06
vg1019221664 sf1019150220 10 19221664 3.36E-06 4.41E-06
vg1207302951 sf1207300358 12 7302951 3.93E-06 1.65E-06
vg0225887862 sf0225881993 2 25887862 6.58E-06 NA
vg1216729892 sf1216723846 12 16729892 NA 2.66E-06
vg0910259535 sf0910258534 9 10259535 NA 3.34E-06
vg1208174078 sf1208171484 12 8174078 NA 4.87E-06