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 mr1822 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
vg0434750995 sf0434565887 4 34750995 4.96E-08 4.96E-08
vg1218763524 sf1218734959 12 18763524 1.52E-07 1.52E-07
vg1209219062 sf1209216471 12 9219062 5.81E-07 5.81E-07
vg0712004641 sf0712003647 7 12004641 1.64E-06 1.64E-06
vg0801497811 sf0801496813 8 1497811 2.60E-06 2.60E-06
vg0608659334 sf0608658335 6 8659334 3.64E-06 3.64E-06
vg0228078795 sf0228072926 2 28078795 4.10E-06 4.10E-06
vg0618358824 sf0618419129 6 18358824 4.80E-06 4.80E-06