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 mr1435 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
vg0217071444 sf0217065574 2 17071444 5.66E-42 7.00E-30
vg0812023942 sf0812022947 8 12023942 4.30E-18 1.35E-09
vg0213525745 sf0213525741 2 13525745 9.81E-16 1.47E-07
vg0217737467 sf0217731597 2 17737467 2.75E-15 2.62E-10
vg0900337327 sf0900336327 9 337327 8.07E-15 5.93E-08
vg0900336799 sf0900335799 9 336799 1.15E-14 5.37E-08
vg1005364262 sf1005380799 10 5364262 4.08E-14 3.28E-10
vg0216662827 sf0216656957 2 16662827 5.08E-12 2.83E-07
vg1114870126 sf1114406440 11 14870126 7.27E-12 4.47E-08
vg0217678234 sf0217672364 2 17678234 1.22E-11 4.08E-07
vg0217969640 sf0217963771 2 17969640 2.13E-10 1.14E-06
vg0216631549 sf0216625679 2 16631549 5.87E-10 1.61E-06
vg0216223264 sf0216217394 2 16223264 7.07E-10 1.46E-07
vg0217605633 sf0217599763 2 17605633 1.37E-09 3.33E-06
vg0804883931 sf0804882934 8 4883931 2.06E-09 1.68E-06
vg0216721532 sf0216715662 2 16721532 2.38E-09 1.39E-06
vg0216773376 sf0216767506 2 16773376 1.12E-08 3.71E-06
vg0404016698 sf0404012305 4 4016698 3.88E-08 4.06E-07
vg1112889066 sf1112425387 11 12889066 1.94E-07 2.40E-06
vg0404020437 sf0404016044 4 4020437 1.98E-07 1.00E-06
vg0220342684 sf0220336816 2 20342684 8.78E-07 NA