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 mr1453 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
vg0332498725 sf0332491598 3 32498725 7.81E-12 NA
vg0922565216 sf0922564735 9 22565216 1.28E-11 NA
vg0329834062 sf0329827101 3 29834062 2.27E-11 NA
vg0517778734 sf0517718220 5 17778734 9.57E-11 NA
vg0705079618 sf0705078619 7 5079618 1.38E-10 NA
vg0917265313 sf0917264312 9 17265313 1.36E-09 NA
vg1112946292 sf1112482613 11 12946292 2.85E-09 NA
vg1110037503 sf1110032080 11 10037503 1.23E-07 NA
vg0825781053 sf0825778339 8 25781053 2.81E-07 NA
vg0139349964 sf0139348921 1 39349964 3.60E-07 NA
vg1114869505 sf1114405819 11 14869505 4.25E-07 NA
vg0625073430 sf0625072433 6 25073430 5.25E-07 1.57E-06
vg1222877698 sf1222844138 12 22877698 NA 2.65E-06