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 mr1274 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
vg0605262883 sf0605261884 6 5262883 1.35E-44 2.28E-23
vg0605311849 sf0605310850 6 5311849 9.52E-41 1.68E-25
vg0605162589 sf0605161590 6 5162589 1.21E-17 2.72E-08
vg0600826406 sf0600825407 6 826406 2.32E-17 NA
vg0604874744 sf0604873745 6 4874744 1.24E-15 1.72E-06
vg0605126671 sf0605125672 6 5126671 1.95E-15 3.33E-07
vg0919681714 sf0919681304 9 19681714 4.33E-15 NA
vg0603680086 sf0603679087 6 3680086 7.11E-15 NA
vg0605412605 sf0605411606 6 5412605 3.21E-14 1.92E-07
vg0209216559 sf0209216557 2 9216559 1.86E-11 NA
vg0607535749 sf0607534750 6 7535749 3.85E-11 2.05E-06
vg0605917767 sf0605916768 6 5917767 4.59E-11 2.58E-06
vg0920815305 sf0920814824 9 20815305 1.54E-10 2.17E-07
vg0702648883 sf0702647884 7 2648883 1.41E-08 NA
vg0605617450 sf0605616451 6 5617450 NA 1.66E-06
vg1214314544 sf1214311884 12 14314544 NA 3.27E-06