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 mr1304 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
vg0726879232 sf0726878238 7 26879232 4.97E-28 8.68E-07
vg0310812075 sf0310810793 3 10812075 1.59E-27 NA
vg0816155031 sf0816152317 8 16155031 7.75E-27 NA
vg1018654736 sf1018583294 10 18654736 1.02E-26 3.52E-06
vg0529502181 sf0529439536 5 29502181 8.70E-26 NA
vg0725923094 sf0725922100 7 25923094 6.82E-24 NA
vg0808100775 sf0808099779 8 8100775 3.34E-23 NA
vg0334721774 sf0334714644 3 34721774 1.29E-22 2.03E-06
vg0726195894 sf0726194900 7 26195894 NA 1.67E-07
vg0726187838 sf0726186844 7 26187838 NA 4.33E-07
vg0230170128 sf0230164259 2 30170128 NA 1.05E-06
vg1214600105 sf1214597445 12 14600105 NA 1.78E-06
vg1128141588 sf1127618367 11 28141588 NA 1.83E-06
vg0909336609 sf0909335608 9 9336609 NA 2.41E-06
vg0421498214 sf0421326265 4 21498214 NA 2.67E-06
vg0509682776 sf0509682705 5 9682776 NA 4.23E-06
vg0510444945 sf0510444874 5 10444945 NA 4.24E-06
vg0819424621 sf0819421908 8 19424621 NA 4.36E-06
vg0421497689 sf0421325740 4 21497689 NA 4.39E-06
vg0729243816 sf0729242824 7 29243816 NA 4.76E-06
vg0510636377 sf0510636306 5 10636377 NA 4.96E-06