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 mr1589 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
vg0222717971 sf0222712102 2 22717971 1.57E-49 5.48E-30
vg0222747179 sf0222741310 2 22747179 2.54E-49 1.35E-30
vg0906971590 sf0906970590 9 6971590 4.70E-34 2.72E-06
vg0702487079 sf0702486080 7 2487079 4.90E-31 5.04E-06
vg0526062179 sf0525999599 5 26062179 6.87E-30 NA
vg1110107976 sf1110102553 11 10107976 3.01E-29 3.27E-06
vg1110318502 sf1110313079 11 10318502 3.34E-28 2.62E-07
vg0316028751 sf0316027398 3 16028751 1.81E-26 4.32E-06
vg0222693356 sf0222687487 2 22693356 8.28E-25 3.94E-08
vg0434765473 sf0434580364 4 34765473 4.25E-22 NA
vg0222398309 sf0222392440 2 22398309 6.58E-22 2.63E-07
vg0222573327 sf0222567458 2 22573327 NA 2.13E-13
vg0222724225 sf0222718356 2 22724225 NA 1.11E-12
vg0224872829 sf0224866960 2 24872829 NA 2.89E-08
vg0222729853 sf0222723984 2 22729853 NA 6.75E-08
vg0222634177 sf0222628308 2 22634177 NA 7.85E-08
vg0224775330 sf0224769461 2 24775330 NA 4.47E-07
vg0224239570 sf0224233701 2 24239570 NA 6.44E-07
vg0222828580 sf0222822711 2 22828580 NA 7.11E-07
vg0224832469 sf0224826600 2 24832469 NA 1.05E-06
vg1104754419 sf1104750321 11 4754419 NA 1.55E-06
vg0223507824 sf0223501955 2 23507824 NA 2.42E-06
vg0224508452 sf0224502583 2 24508452 NA 2.53E-06
vg0519674799 sf0519612283 5 19674799 NA 3.80E-06
vg0224640322 sf0224634453 2 24640322 NA 4.46E-06
vg1200551682 sf1200550682 12 551682 NA 4.55E-06