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 mr1117 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
vg0501780209 sf0501780192 5 1780209 2.53E-12 3.01E-09
vg0219890874 sf0219885006 2 19890874 5.99E-10 3.00E-08
vg1008520987 sf1008449849 10 8520987 3.36E-08 7.89E-07
vg0227977382 sf0227971513 2 27977382 3.52E-08 NA
vg1009690319 sf1009619140 10 9690319 3.56E-08 8.95E-07
vg1006845318 sf1006860941 10 6845318 4.82E-08 1.14E-07
vg0216716103 sf0216710233 2 16716103 8.40E-08 1.15E-06
vg0312535741 sf0312534459 3 12535741 1.06E-07 1.91E-06
vg0916693881 sf0916692880 9 16693881 1.39E-07 4.52E-06
vg0402229157 sf0402224752 4 2229157 1.63E-07 1.79E-06
vg1220166852 sf1220138294 12 20166852 6.02E-07 4.04E-06
vg0912032927 sf0912031926 9 12032927 1.04E-06 NA
vg0827543233 sf0827540519 8 27543233 2.10E-06 4.89E-06
vg0111460968 sf0111459944 1 11460968 2.35E-06 1.96E-06
vg0334402323 sf0334395193 3 34402323 2.56E-06 4.19E-06
vg1216729892 sf1216723846 12 16729892 4.13E-06 2.16E-06
vg0504913720 sf0504913698 5 4913720 4.83E-06 NA
vg0504314615 sf0504314592 5 4314615 NA 2.20E-06