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 mr1037 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
vg0402389835 sf0402385430 4 2389835 9.40E-45 1.56E-13
vg0205658378 sf0205658378 2 5658378 1.20E-39 2.68E-07
vg1204503516 sf1204502504 12 4503516 7.60E-38 NA
vg0522015078 sf0521952520 5 22015078 4.64E-36 NA
vg0233990252 sf0233984383 2 33990252 4.77E-35 NA
vg0402373652 sf0402369247 4 2373652 NA 1.33E-08
vg1223626565 sf1223593021 12 23626565 NA 3.11E-07
vg0402308314 sf0402303909 4 2308314 NA 5.12E-07
vg0402386328 sf0402381923 4 2386328 NA 5.96E-07
vg0404609763 sf0404605366 4 4609763 NA 6.09E-07
vg0401972146 sf0401967742 4 1972146 NA 6.87E-07
vg1002324925 sf1002323902 10 2324925 NA 9.85E-07
vg0620427074 sf0620426077 6 20427074 NA 9.97E-07
vg0619650681 sf0619649684 6 19650681 NA 1.06E-06
vg0205660004 sf0205660004 2 5660004 NA 1.08E-06
vg0921454670 sf0921454189 9 21454670 NA 1.49E-06
vg1105648980 sf1105644732 11 5648980 NA 2.56E-06
vg0205657255 sf0205657255 2 5657255 NA 2.62E-06
vg0621705466 sf0621704469 6 21705466 NA 3.08E-06
vg0620431139 sf0620430142 6 20431139 NA 4.03E-06
vg1221482388 sf1221448935 12 21482388 NA 7.38E-06