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 mr1111 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
vg0610752378 sf0610751379 6 10752378 3.60E-14 3.60E-14
vg0610460953 sf0610459954 6 10460953 1.02E-09 1.02E-09
vg0403922278 sf0403917884 4 3922278 9.82E-08 9.83E-08
vg1006614973 sf1006630596 10 6614973 8.35E-07 8.35E-07
vg0629851797 sf0629850799 6 29851797 1.30E-06 1.30E-06
vg1127461949 sf1126990336 11 27461949 1.60E-06 1.60E-06
vg0725081143 sf0725080149 7 25081143 1.79E-06 1.79E-06
vg0135554286 sf0135553243 1 35554286 2.58E-06 2.58E-06
vg1125612916 sf1125146755 11 25612916 3.75E-06 3.75E-06
vg0432436067 sf0432250958 4 32436067 4.00E-06 4.00E-06
vg0707975245 sf0707974250 7 7975245 4.37E-06 4.37E-06
vg0223178015 sf0223172146 2 23178015 4.54E-06 4.54E-06
vg1117961302 sf1117495160 11 17961302 4.59E-06 4.59E-06
vg0228468795 sf0228462926 2 28468795 4.62E-06 4.62E-06
vg0409773871 sf0409764569 4 9773871 4.95E-06 4.96E-06