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 mr1793 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
vg0802260819 sf0802259822 8 2260819 3.94E-35 NA
vg1109440009 sf1109434586 11 9440009 1.41E-34 NA
vg0608185060 sf0608184061 6 8185060 1.37E-33 NA
vg0919822474 sf0919821993 9 19822474 1.45E-33 8.66E-06
vg0132861439 sf0132860395 1 32861439 1.98E-33 NA
vg0919811255 sf0919810774 9 19811255 1.23E-32 2.76E-06
vg0920086430 sf0920085949 9 20086430 2.33E-32 NA
vg0202720508 sf0202720506 2 2720508 2.01E-30 7.47E-07
vg0202698817 sf0202698815 2 2698817 NA 1.31E-08
vg0317140190 sf0317139004 3 17140190 NA 1.53E-07
vg0414275568 sf0414266281 4 14275568 NA 1.37E-06
vg0421333379 sf0421161433 4 21333379 NA 2.25E-06
vg0208546299 sf0208546298 2 8546299 NA 2.40E-06
vg1000109717 sf1000108717 10 109717 NA 2.54E-06
vg0314987126 sf0314985773 3 14987126 NA 2.57E-06
vg0315004688 sf0315003335 3 15004688 NA 2.85E-06
vg0207187753 sf0207187753 2 7187753 NA 8.86E-06