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
vg0222717971 sf0222712102 2 22717971 4.61E-49 2.65E-28
vg0222747179 sf0222741310 2 22747179 8.42E-49 6.75E-29
vg0906971590 sf0906970590 9 6971590 5.54E-44 8.42E-06
vg0702487079 sf0702486080 7 2487079 6.81E-43 1.79E-07
vg0525793764 sf0525731185 5 25793764 1.09E-41 NA
vg0529002068 sf0528939423 5 29002068 1.51E-40 9.22E-07
vg1110107976 sf1110102553 11 10107976 7.85E-40 4.61E-07
vg0222897061 sf0222891192 2 22897061 1.29E-38 7.05E-12
vg0721347769 sf0721346776 7 21347769 1.29E-37 2.75E-06
vg0222673217 sf0222667348 2 22673217 3.62E-36 2.38E-11
vg0503505574 sf0503505551 5 3505574 4.35E-36 9.78E-07
vg0503964542 sf0503964519 5 3964542 7.81E-34 NA
vg0316028751 sf0316027398 3 16028751 2.42E-33 1.54E-06
vg0434765473 sf0434580364 4 34765473 4.13E-29 2.67E-07
vg0434789415 sf0434604306 4 34789415 8.84E-29 1.76E-07
vg0222573327 sf0222567458 2 22573327 NA 2.56E-10
vg0222677953 sf0222672084 2 22677953 NA 1.23E-07
vg0224013851 sf0224007982 2 24013851 NA 1.31E-07
vg0232358383 sf0232352514 2 32358383 NA 2.60E-07
vg0726600658 sf0726599664 7 26600658 NA 4.69E-07
vg0222623115 sf0222617246 2 22623115 NA 1.30E-06
vg0224872829 sf0224866960 2 24872829 NA 2.32E-06
vg0227413767 sf0227407898 2 27413767 NA 2.57E-06
vg0322133332 sf0322131839 3 22133332 NA 2.82E-06
vg0222398309 sf0222392440 2 22398309 NA 3.04E-06
vg0103854099 sf0103853099 1 3854099 NA 3.09E-06