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 mr1221 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
vg0610275164 sf0610274165 6 10275164 3.43E-41 2.75E-22
vg0610462485 sf0610461486 6 10462485 4.01E-33 1.29E-19
vg0612914787 sf0612913788 6 12914787 9.39E-26 2.32E-07
vg0617359224 sf0617358227 6 17359224 6.58E-23 4.97E-06
vg0629122299 sf0629121301 6 29122299 1.24E-18 1.18E-07
vg0611882742 sf0611881743 6 11882742 1.42E-18 7.25E-09
vg0610555125 sf0610554126 6 10555125 2.08E-18 8.37E-13
vg0610278393 sf0610277394 6 10278393 3.91E-16 1.17E-11
vg0609654677 sf0609653678 6 9654677 6.24E-16 2.20E-09
vg0610606146 sf0610605147 6 10606146 8.84E-14 1.35E-11
vg0610590324 sf0610589325 6 10590324 3.27E-13 2.63E-08
vg0610036949 sf0610035950 6 10036949 1.71E-12 1.53E-09
vg0717519774 sf0717518781 7 17519774 6.52E-11 3.06E-06
vg0609457229 sf0609456230 6 9457229 2.24E-10 2.14E-07
vg0609862613 sf0609861614 6 9862613 2.07E-09 5.35E-07
vg0527112841 sf0527050197 5 27112841 NA 6.85E-08
vg1020189984 sf1020118466 10 20189984 NA 3.05E-07
vg0610873728 sf0610872729 6 10873728 NA 1.19E-06
vg1216521167 sf1216518460 12 16521167 NA 1.75E-06
vg0610792532 sf0610791533 6 10792532 NA 2.25E-06