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 mr1334 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
vg1220340557 sf1220311999 12 20340557 8.69E-20 4.30E-15
vg1220875510 sf1220842059 12 20875510 8.30E-16 1.62E-11
vg1220236732 sf1220208174 12 20236732 1.62E-15 5.17E-12
vg1220221344 sf1220192786 12 20221344 7.27E-15 8.23E-12
vg1219955678 sf1219927148 12 19955678 1.47E-14 1.70E-11
vg1220393967 sf1220365409 12 20393967 2.15E-14 1.35E-11
vg1220179248 sf1220150690 12 20179248 6.33E-14 6.46E-10
vg1221084747 sf1221051297 12 21084747 1.14E-13 7.06E-11
vg1220529160 sf1220500602 12 20529160 1.44E-13 1.53E-10
vg1220867141 sf1220833690 12 20867141 4.65E-13 3.27E-11
vg1221035693 sf1221002243 12 21035693 1.41E-12 3.59E-10
vg0807919580 sf0807918584 8 7919580 1.60E-12 3.53E-09
vg1221098483 sf1221065033 12 21098483 1.60E-12 4.51E-09
vg1222195768 sf1222162315 12 22195768 2.00E-12 2.63E-09
vg1220875140 sf1220841689 12 20875140 2.60E-12 7.75E-11
vg1207982009 sf1207979415 12 7982009 3.05E-12 5.31E-09
vg0915376133 sf0915375132 9 15376133 6.84E-12 6.39E-09
vg1220380232 sf1220351674 12 20380232 7.72E-12 6.43E-09
vg1220015795 sf1219987237 12 20015795 1.16E-11 1.81E-09
vg1221050840 sf1221017390 12 21050840 1.82E-11 4.03E-09
vg1220254803 sf1220226245 12 20254803 1.37E-10 1.51E-09
vg1221083115 sf1221049665 12 21083115 1.58E-08 4.89E-10