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 mr1206 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
vg0900708420 sf0900707420 9 708420 2.02E-09 NA
vg0801919808 sf0801918811 8 1919808 5.13E-09 NA
vg0826402159 sf0826399445 8 26402159 6.24E-09 5.81E-06
vg0826228501 sf0826225787 8 26228501 8.06E-09 4.48E-06
vg0904278800 sf0904277800 9 4278800 8.59E-09 NA
vg1217424379 sf1217418334 12 17424379 9.25E-09 NA
vg1210109915 sf1210107326 12 10109915 3.87E-08 3.28E-06
vg0915815139 sf0915814138 9 15815139 6.97E-08 1.45E-06
vg0902343614 sf0902342614 9 2343614 1.26E-07 1.74E-06
vg1011333524 sf1011262344 10 11333524 8.37E-07 3.61E-06
vg0402290555 sf0402286150 4 2290555 4.54E-06 5.52E-07
vg1004059501 sf1004058477 10 4059501 5.11E-06 9.24E-06
vg1219590404 sf1219561874 12 19590404 7.13E-06 3.59E-07
vg0616884771 sf0616883774 6 16884771 NA 2.83E-06
vg1219748904 sf1219720374 12 19748904 NA 3.45E-06