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 mr1611 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
vg0604160684 sf0604159685 6 4160684 7.42E-35 1.70E-10
vg0604234049 sf0604233050 6 4234049 5.88E-31 1.60E-10
vg0311356904 sf0311355622 3 11356904 2.21E-30 NA
vg0604236666 sf0604235667 6 4236666 2.37E-30 1.56E-11
vg0527396896 sf0527334252 5 27396896 2.49E-29 NA
vg0314622952 sf0314621639 3 14622952 4.66E-29 2.77E-07
vg0311214331 sf0311213049 3 11214331 6.73E-28 5.01E-07
vg0329083556 sf0329076608 3 29083556 9.80E-25 1.89E-07
vg0118369451 sf0118368405 1 18369451 1.61E-24 1.48E-06
vg1022854220 sf1022782693 10 22854220 1.75E-24 8.14E-07
vg0314873937 sf0314872584 3 14873937 3.00E-24 2.76E-08
vg0522356134 sf0522293575 5 22356134 1.19E-23 2.26E-06
vg0526967577 sf0526904933 5 26967577 1.03E-22 3.95E-06
vg0604726687 sf0604725688 6 4726687 NA 2.58E-08
vg1126430567 sf1125958980 11 26430567 NA 3.05E-07
vg0422478558 sf0422293445 4 22478558 NA 1.22E-06
vg1125386074 sf1124919913 11 25386074 NA 1.26E-06
vg1001104739 sf1001103715 10 1104739 NA 1.38E-06
vg0326933756 sf0326926809 3 26933756 NA 1.58E-06
vg0403780245 sf0403775850 4 3780245 NA 2.53E-06
vg0404932550 sf0404927989 4 4932550 NA 2.62E-06
vg0422513974 sf0422328861 4 22513974 NA 2.77E-06
vg0208546299 sf0208546298 2 8546299 NA 3.49E-06
vg0702783022 sf0702782023 7 2783022 NA 3.58E-06
vg1122067670 sf1121601541 11 22067670 NA 3.67E-06
vg0706319441 sf0706318444 7 6319441 NA 4.02E-06