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 mr1551 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
vg0702524727 sf0702523728 7 2524727 5.18E-30 2.94E-06
vg0304897093 sf0304896095 3 4897093 1.25E-29 NA
vg1015460096 sf1015388864 10 15460096 1.79E-29 NA
vg0206385997 sf0206385997 2 6385997 2.67E-29 NA
vg0420441927 sf0420269971 4 20441927 3.42E-29 NA
vg0822230941 sf0822228228 8 22230941 2.11E-26 2.50E-06
vg0407782160 sf0407777428 4 7782160 NA 5.65E-07
vg0311279294 sf0311278012 3 11279294 NA 7.72E-07
vg0801858513 sf0801857516 8 1858513 NA 1.78E-06
vg0801877570 sf0801876573 8 1877570 NA 2.88E-06
vg0621350656 sf0621349659 6 21350656 NA 8.96E-06