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 mr1543 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
vg0916441676 sf0916440675 9 16441676 1.06E-09 NA
vg0324461657 sf0324459736 3 24461657 4.46E-09 NA
vg0417345266 sf0417173309 4 17345266 5.03E-09 NA
vg1102274880 sf1102270738 11 2274880 1.04E-08 NA
vg0320737660 sf0320736170 3 20737660 1.92E-08 NA
vg0619014811 sf0619013814 6 19014811 1.38E-07 NA
vg0904124928 sf0904123928 9 4124928 1.25E-06 4.24E-06
vg1222506866 sf1222473305 12 22506866 1.77E-06 NA
vg0417640422 sf0417468463 4 17640422 3.74E-06 NA
vg0112718109 sf0112717083 1 12718109 6.20E-06 NA