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 mr1425 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
vg0321870228 sf0321868738 3 21870228 1.61E-11 1.42E-08
vg1209644048 sf1209641457 12 9644048 2.32E-11 3.63E-07
vg1212529629 sf1212526968 12 12529629 7.92E-09 NA
vg1212617202 sf1212614541 12 12617202 1.57E-08 NA
vg1200344922 sf1200343922 12 344922 3.20E-08 NA
vg0802944461 sf0802943464 8 2944461 1.08E-07 9.07E-07
vg0220461014 sf0220455146 2 20461014 3.14E-07 1.11E-06
vg1107749329 sf1107745074 11 7749329 8.11E-07 1.10E-06
vg0802257334 sf0802256337 8 2257334 2.36E-06 3.92E-06
vg0803057970 sf0803056973 8 3057970 8.97E-06 NA
vg1107765430 sf1107761175 11 7765430 9.39E-06 NA