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 mr1305 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
vg0334986236 sf0334979106 3 34986236 2.28E-10 3.77E-09
vg1000284248 sf1000283248 10 284248 3.52E-09 6.24E-06
vg0334732771 sf0334725641 3 34732771 4.57E-09 1.86E-07
vg0334916269 sf0334909139 3 34916269 8.69E-09 2.96E-06
vg1012891999 sf1012820814 10 12891999 1.77E-07 4.04E-08
vg0911067540 sf0911066539 9 11067540 3.76E-07 3.83E-06
vg0221873638 sf0221867769 2 21873638 6.44E-07 4.97E-06
vg0628393090 sf0628392092 6 28393090 9.65E-07 3.18E-06
vg0524244054 sf0524181473 5 24244054 1.73E-06 1.31E-06
vg0325762988 sf0325761006 3 25762988 NA 1.11E-06