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 mr1449 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
vg1219717603 sf1219689073 12 19717603 2.81E-19 9.72E-06
vg0522579477 sf0522516919 5 22579477 4.36E-18 NA
vg0141925023 sf0141923980 1 41925023 5.27E-18 NA
vg0919305288 sf0919304878 9 19305288 7.34E-18 NA
vg0104311438 sf0104310438 1 4311438 1.12E-17 NA
vg0626134561 sf0626133564 6 26134561 1.16E-13 NA
vg1117639792 sf1117173648 11 17639792 1.25E-13 NA
vg1217056435 sf1217050390 12 17056435 NA 1.91E-07
vg0224703299 sf0224697430 2 24703299 NA 4.49E-06