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 mr1480 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
vg0822031104 sf0822028391 8 22031104 1.11E-59 NA
vg0628590475 sf0628589477 6 28590475 2.70E-59 NA
vg0823360400 sf0823357687 8 23360400 1.19E-58 4.21E-06
vg0205481873 sf0205481873 2 5481873 1.22E-57 NA
vg0726354661 sf0726353667 7 26354661 1.38E-57 NA
vg0523014690 sf0522952131 5 23014690 5.09E-57 NA
vg0230026462 sf0230020593 2 30026462 2.27E-54 1.17E-06
vg0205284721 sf0205284719 2 5284721 NA 3.16E-08
vg0718117888 sf0718116895 7 18117888 NA 5.42E-08
vg0808042725 sf0808041729 8 8042725 NA 5.81E-08
vg0142446761 sf0142445717 1 42446761 NA 5.92E-07
vg0718661127 sf0718660134 7 18661127 NA 1.42E-06
vg0234416765 sf0234410896 2 34416765 NA 1.99E-06
vg0234326223 sf0234320354 2 34326223 NA 2.18E-06
vg0722173629 sf0722172636 7 22173629 NA 2.53E-06
vg0207959950 sf0207959949 2 7959950 NA 3.17E-06
vg0605538060 sf0605537061 6 5538060 NA 3.57E-06
vg0628613000 sf0628612002 6 28613000 NA 3.85E-06
vg0721765273 sf0721764280 7 21765273 NA 4.71E-06
vg1006743994 sf1006759617 10 6743994 NA 8.48E-06