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 mr1098 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
vg0222743508 sf0222737639 2 22743508 3.41E-57 8.19E-34
vg0222723992 sf0222718123 2 22723992 8.96E-57 2.30E-34
vg0906971590 sf0906970590 9 6971590 5.68E-46 3.87E-06
vg0222646311 sf0222640442 2 22646311 4.26E-45 7.15E-14
vg0222679274 sf0222673405 2 22679274 5.08E-44 2.53E-11
vg0505964521 sf0505964460 5 5964521 1.43E-41 2.78E-07
vg0700414199 sf0700413199 7 414199 2.32E-41 3.53E-06
vg0524971409 sf0524908824 5 24971409 1.35E-36 4.81E-06
vg1200741644 sf1200740644 12 741644 5.75E-33 3.39E-06
vg0518290594 sf0518230080 5 18290594 4.82E-31 2.02E-06
vg0907026290 sf0907025290 9 7026290 3.43E-29 8.91E-07
vg0222725003 sf0222719134 2 22725003 NA 8.72E-12
vg0224552398 sf0224546529 2 24552398 NA 5.28E-09
vg0224817933 sf0224812064 2 24817933 NA 2.86E-08
vg0222271516 sf0222265647 2 22271516 NA 1.82E-07
vg0141182631 sf0141181588 1 41182631 NA 1.88E-07
vg0214216570 sf0214210700 2 14216570 NA 7.86E-07
vg0709372324 sf0709371330 7 9372324 NA 1.09E-06
vg0141112730 sf0141111687 1 41112730 NA 1.16E-06
vg0223663745 sf0223657876 2 23663745 NA 1.36E-06
vg0224775330 sf0224769461 2 24775330 NA 1.91E-06
vg0525568162 sf0525505583 5 25568162 NA 2.05E-06
vg0222677953 sf0222672084 2 22677953 NA 2.17E-06
vg0716928375 sf0716927382 7 16928375 NA 2.55E-06
vg0224190332 sf0224184463 2 24190332 NA 3.03E-06
vg0223997442 sf0223991573 2 23997442 NA 3.05E-06
vg0221010615 sf0221004747 2 21010615 NA 3.40E-06
vg0721709577 sf0721708584 7 21709577 NA 4.76E-06