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 mr1938 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
vg0526374318 sf0526311681 5 26374318 2.79E-19 1.04E-06
vg0525640106 sf0525577527 5 25640106 3.60E-18 6.17E-07
vg0301533591 sf0301532587 3 1533591 3.62E-17 NA
vg0318056748 sf0318055530 3 18056748 8.60E-17 NA
vg0232755756 sf0232749887 2 32755756 1.18E-16 NA
vg1101083366 sf1101082367 11 1083366 1.36E-16 NA
vg1219590404 sf1219561874 12 19590404 NA 1.19E-06
vg0525068753 sf0525006168 5 25068753 NA 1.46E-06
vg1212822297 sf1212819636 12 12822297 NA 3.01E-06
vg0509824684 sf0509824613 5 9824684 NA 4.32E-06