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 mr1336 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
vg0208736544 sf0208736543 2 8736544 9.79E-15 NA
vg0726319060 sf0726318066 7 26319060 1.23E-14 4.41E-06
vg0104006648 sf0104005648 1 4006648 2.16E-13 NA
vg0817431818 sf0817429104 8 17431818 6.99E-13 NA
vg0215273039 sf0215267169 2 15273039 2.18E-12 NA
vg1111565611 sf1111559928 11 11565611 1.12E-10 NA
vg0620057664 sf0620056667 6 20057664 7.53E-10 NA
vg1104756884 sf1104752786 11 4756884 2.07E-09 2.55E-07
vg1104752147 sf1104748049 11 4752147 NA 3.36E-07
vg0222221610 sf0222215741 2 22221610 NA 1.16E-06
vg1122942578 sf1122476449 11 22942578 NA 1.89E-06
vg0433005106 sf0432819992 4 33005106 NA 2.48E-06
vg0819980575 sf0819977862 8 19980575 NA 2.58E-06
vg0601508115 sf0601507116 6 1508115 NA 2.73E-06
vg0100695213 sf0100694213 1 695213 NA 4.70E-06
vg1122878285 sf1122412156 11 22878285 NA 5.05E-06