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 mr1649 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
vg0325710457 sf0325708475 3 25710457 2.06E-10 2.06E-10
vg0310982373 sf0310981091 3 10982373 3.09E-08 3.09E-08
vg1105209609 sf1105205420 11 5209609 3.22E-08 3.22E-08
vg1002824620 sf1002823597 10 2824620 1.88E-07 1.88E-07
vg0710938505 sf0710937511 7 10938505 3.22E-07 3.22E-07
vg1127985849 sf1127514235 11 27985849 3.60E-07 3.60E-07
vg1121711093 sf1121244970 11 21711093 4.64E-07 4.64E-07
vg0609841754 sf0609840755 6 9841754 6.15E-07 6.15E-07
vg0623034324 sf0623033327 6 23034324 6.57E-07 6.57E-07
vg0202817095 sf0202817093 2 2817095 9.47E-07 9.47E-07
vg1017190380 sf1017119153 10 17190380 1.97E-06 1.97E-06
vg1012708940 sf1012637755 10 12708940 2.32E-06 2.32E-06
vg0400345487 sf0400344487 4 345487 2.63E-06 2.63E-06
vg0221782106 sf0221776237 2 21782106 2.73E-06 2.73E-06
vg0713887346 sf0713886353 7 13887346 2.87E-06 2.87E-06
vg0720236543 sf0720235550 7 20236543 3.58E-06 3.58E-06
vg1005691507 sf1005708045 10 5691507 3.62E-06 3.62E-06
vg0906972834 sf0906971834 9 6972834 4.10E-06 4.10E-06