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 mr1091 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
vg0610648813 sf0610647814 6 10648813 9.04E-09 1.64E-06
vg0516417324 sf0516359806 5 16417324 1.02E-08 NA
vg0611683955 sf0611682956 6 11683955 1.09E-08 NA
vg0610197332 sf0610196333 6 10197332 1.15E-08 NA
vg0610752378 sf0610751379 6 10752378 1.18E-08 3.44E-07
vg0139810181 sf0139809138 1 39810181 1.56E-08 4.25E-06
vg0609350915 sf0609349916 6 9350915 4.25E-08 2.54E-08
vg0610766790 sf0610765791 6 10766790 1.78E-07 NA
vg1208226889 sf1208224294 12 8226889 2.73E-07 3.93E-06
vg0618366551 sf0618365554 6 18366551 8.92E-07 2.25E-06
vg0419122412 sf0418950450 4 19122412 1.44E-06 1.08E-06
vg0325724242 sf0325722260 3 25724242 6.59E-06 3.79E-06
vg1115365932 sf1114902246 11 15365932 NA 7.29E-07