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 mr1848 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
vg0519668538 sf0519606022 5 19668538 8.53E-09 8.53E-09
vg0224747617 sf0224741748 2 24747617 2.84E-08 2.84E-08
vg0211856727 sf0211856723 2 11856727 4.02E-08 4.02E-08
vg0143071069 sf0143070025 1 43071069 1.62E-07 1.62E-07
vg1126957950 sf1126486337 11 26957950 2.23E-07 2.23E-07
vg0806250261 sf0806249266 8 6250261 4.04E-07 4.04E-07
vg1015871199 sf1015799969 10 15871199 4.56E-07 4.56E-07
vg0911094465 sf0911093464 9 11094465 4.83E-07 4.83E-07
vg0335273089 sf0335265958 3 35273089 5.29E-07 5.29E-07
vg0624773677 sf0624772680 6 24773677 9.47E-07 9.47E-07
vg0506492322 sf0506492263 5 6492322 1.03E-06 1.03E-06
vg0528846263 sf0528783618 5 28846263 1.31E-06 1.32E-06
vg0528812466 sf0528749821 5 28812466 1.48E-06 1.48E-06
vg0124201785 sf0124200741 1 24201785 1.49E-06 1.49E-06
vg1209903866 sf1209901276 12 9903866 1.76E-06 1.76E-06
vg0414573200 sf0414563914 4 14573200 1.86E-06 1.86E-06
vg0402986544 sf0402982150 4 2986544 2.50E-06 2.50E-06
vg0315761422 sf0315760069 3 15761422 2.85E-06 2.85E-06
vg0609657256 sf0609656257 6 9657256 3.45E-06 3.45E-06
vg0522597893 sf0522535336 5 22597893 3.65E-06 3.65E-06