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 mr1876 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
vg0123685482 sf0123684438 1 23685482 4.00E-09 NA
vg0726964336 sf0726963342 7 26964336 1.01E-08 NA
vg1104966222 sf1104962033 11 4966222 2.33E-08 NA
vg1210166587 sf1210163998 12 10166587 5.00E-08 NA
vg0906503065 sf0906502065 9 6503065 8.95E-08 3.74E-06
vg0726847020 sf0726846026 7 26847020 1.36E-07 NA
vg0431655631 sf0431470524 4 31655631 6.18E-07 4.83E-06
vg0514370755 sf0514313298 5 14370755 4.63E-06 4.92E-06
vg0805469573 sf0805468576 8 5469573 8.15E-06 4.01E-06
vg0302293724 sf0302292720 3 2293724 NA 5.71E-06