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 mr1662 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
vg1125476275 sf1125010114 11 25476275 1.59E-25 7.64E-18
vg0432437759 sf0432252650 4 32437759 7.99E-15 7.05E-08
vg1126386642 sf1125915055 11 26386642 8.31E-13 1.51E-10
vg1125322548 sf1124856388 11 25322548 3.76E-12 5.56E-11
vg0507714473 sf0507714414 5 7714473 1.65E-11 1.50E-06
vg1114596184 sf1114132502 11 14596184 6.69E-10 1.70E-06
vg1126547985 sf1126076400 11 26547985 1.10E-09 1.95E-06
vg1125471041 sf1125004880 11 25471041 6.75E-09 2.00E-07
vg1126979494 sf1126507881 11 26979494 1.19E-08 7.24E-07
vg1125479021 sf1125012860 11 25479021 1.46E-08 2.10E-07
vg1125473544 sf1125007383 11 25473544 2.76E-08 4.06E-07
vg1219745087 sf1219716557 12 19745087 3.02E-08 1.48E-06
vg1126550593 sf1126079008 11 26550593 4.21E-08 3.29E-06
vg1126329129 sf1125857542 11 26329129 1.48E-07 4.06E-06
vg1125089136 sf1124622976 11 25089136 4.10E-07 1.63E-06
vg1124474541 sf1124008381 11 24474541 6.00E-06 1.50E-06
vg1127691454 sf1127219841 11 27691454 6.55E-06 3.21E-06
vg1125419021 sf1124952860 11 25419021 NA 2.39E-07
vg0414233780 sf0414224493 4 14233780 NA 2.16E-06
vg1125596619 sf1125130458 11 25596619 NA 3.91E-06