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 mr1350 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
vg1209083240 sf1209080649 12 9083240 5.76E-08 NA
vg0227151439 sf0227145570 2 27151439 5.01E-07 2.41E-06
vg1209095184 sf1209092593 12 9095184 2.03E-06 NA
vg0408377327 sf0408372601 4 8377327 8.13E-06 7.60E-06
vg0729363260 sf0729362268 7 29363260 NA 1.18E-06
vg1222927642 sf1222894101 12 22927642 NA 2.35E-06
vg0813651729 sf0813649014 8 13651729 NA 2.79E-06
vg0807648774 sf0807647779 8 7648774 NA 3.09E-06
vg0420181217 sf0420009255 4 20181217 NA 5.26E-06