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 mr1510 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
vg0809843322 sf0809842326 8 9843322 6.39E-11 NA
vg0218633626 sf0218627757 2 18633626 1.10E-10 NA
vg0504695747 sf0504695724 5 4695747 1.77E-10 NA
vg0501354532 sf0501354516 5 1354532 2.22E-10 NA
vg0500069986 sf0500069986 5 69986 2.35E-10 NA
vg0806499371 sf0806498376 8 6499371 8.07E-10 2.31E-06
vg0401135977 sf0401131527 4 1135977 2.85E-08 NA
vg0814484428 sf0814481714 8 14484428 1.17E-07 NA
vg0715290134 sf0715289141 7 15290134 4.41E-07 4.84E-06
vg0804314979 sf0804313982 8 4314979 5.60E-07 NA
vg0715326471 sf0715325478 7 15326471 9.13E-07 NA
vg0719155095 sf0719154102 7 19155095 NA 1.39E-06
vg0709538360 sf0709537366 7 9538360 NA 2.52E-06
vg1020835773 sf1020764252 10 20835773 NA 3.14E-06
vg0134535445 sf0134534402 1 34535445 NA 9.28E-06