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 mr1008 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
vg0118347734 sf0118346688 1 18347734 4.10E-09 4.10E-09
vg0916734760 sf0916733759 9 16734760 1.09E-08 1.09E-08
vg0901048364 sf0901047364 9 1048364 1.25E-08 1.25E-08
vg0124089174 sf0124088130 1 24089174 1.45E-08 1.45E-08
vg1220059260 sf1220030702 12 20059260 3.62E-08 3.62E-08
vg0901048761 sf0901047761 9 1048761 4.02E-08 4.02E-08
vg0203460456 sf0203460454 2 3460456 5.82E-08 5.82E-08
vg0406224825 sf0406220265 4 6224825 7.45E-08 7.45E-08
vg1003360615 sf1003359592 10 3360615 7.93E-08 7.93E-08
vg1209876216 sf1209873626 12 9876216 8.55E-08 8.55E-08
vg0729253566 sf0729252574 7 29253566 9.66E-08 9.66E-08
vg0112302656 sf0112301630 1 12302656 1.42E-07 1.42E-07
vg0820198596 sf0820195883 8 20198596 3.63E-07 3.63E-07
vg1123222536 sf1122756407 11 23222536 5.99E-07 5.99E-07
vg0522357374 sf0522294815 5 22357374 7.39E-07 7.39E-07
vg1016228574 sf1016157346 10 16228574 7.52E-07 7.52E-07
vg0622642007 sf0622641010 6 22642007 8.43E-07 8.43E-07
vg0138579441 sf0138578398 1 38579441 9.40E-07 9.39E-07
vg1219821279 sf1219792749 12 19821279 1.25E-06 1.25E-06
vg1015657131 sf1015585901 10 15657131 1.89E-06 1.89E-06
vg0130874710 sf0130873666 1 30874710 2.05E-06 2.05E-06