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 mr1496 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
vg0222693356 sf0222687487 2 22693356 1.04E-45 1.14E-24
vg0222739148 sf0222733279 2 22739148 2.94E-27 1.77E-22
vg1110425815 sf1110420360 11 10425815 9.07E-25 7.53E-12
vg0222471248 sf0222465379 2 22471248 1.24E-24 1.44E-08
vg0110400456 sf0110399432 1 10400456 1.26E-22 2.68E-07
vg0906971590 sf0906970590 9 6971590 8.68E-22 2.49E-06
vg0314739384 sf0314738071 3 14739384 1.13E-21 6.48E-09
vg0311965593 sf0311964311 3 11965593 1.74E-21 1.95E-07
vg0335906768 sf0335899637 3 35906768 2.21E-21 4.94E-09
vg0825885835 sf0825883121 8 25885835 2.46E-21 6.50E-08
vg1204550069 sf1204549057 12 4550069 5.14E-21 1.56E-07
vg0505351376 sf0505351354 5 5351376 3.25E-20 1.37E-07
vg0907026290 sf0907025290 9 7026290 6.06E-20 6.61E-08
vg0434789415 sf0434604306 4 34789415 8.17E-19 1.46E-07
vg0819125422 sf0819122709 8 19125422 1.39E-17 2.58E-06
vg0819123966 sf0819121253 8 19123966 5.56E-17 1.74E-07
vg0222952563 sf0222946694 2 22952563 6.61E-16 3.29E-10
vg0141558120 sf0141557077 1 41558120 5.30E-14 1.61E-07
vg0222722554 sf0222716685 2 22722554 NA 3.00E-14
vg0327037726 sf0327030779 3 27037726 NA 3.90E-09
vg1016331604 sf1016260380 10 16331604 NA 7.66E-09
vg0222926098 sf0222920229 2 22926098 NA 8.59E-09
vg0505935594 sf0505935533 5 5935594 NA 2.09E-08
vg0709837237 sf0709836243 7 9837237 NA 3.14E-08
vg0626215270 sf0626214273 6 26215270 NA 5.71E-08
vg0118204544 sf0118203498 1 18204544 NA 1.02E-07
vg0802058938 sf0802057941 8 2058938 NA 1.27E-07
vg0816119183 sf0816116469 8 16119183 NA 2.00E-07
vg1204507349 sf1204506337 12 4507349 NA 3.79E-07
vg0219344371 sf0219338503 2 19344371 NA 9.52E-07
vg0804649551 sf0804648554 8 4649551 NA 2.45E-06