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 mr1623 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
vg0805058036 sf0805057039 8 5058036 2.46E-10 2.25E-06
vg0331822672 sf0331815549 3 31822672 3.89E-10 1.78E-06
vg0724401578 sf0724400584 7 24401578 5.43E-10 NA
vg0619763326 sf0619762329 6 19763326 5.49E-10 NA
vg0713275159 sf0713274166 7 13275159 5.68E-10 NA
vg0304931155 sf0304930157 3 4931155 4.35E-09 2.41E-06
vg0332521913 sf0332514786 3 32521913 1.13E-08 NA
vg1214610078 sf1214607418 12 14610078 6.23E-08 5.51E-07
vg0621001703 sf0621000706 6 21001703 3.28E-07 NA
vg0725311495 sf0725310501 7 25311495 5.91E-07 NA
vg0107647091 sf0107646091 1 7647091 NA 6.60E-09
vg1224600619 sf1224567073 12 24600619 NA 7.26E-07
vg1105609281 sf1105605033 11 5609281 NA 9.21E-07
vg0608598579 sf0608597580 6 8598579 NA 1.85E-06