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 mr1335 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
vg0711878666 sf0711877672 7 11878666 5.63E-10 5.30E-06
vg0711689812 sf0711688818 7 11689812 6.09E-10 4.61E-06
vg1223534586 sf1223501046 12 23534586 1.03E-09 NA
vg0724557789 sf0724556795 7 24557789 1.10E-09 NA
vg0803821174 sf0803820177 8 3821174 1.46E-09 NA
vg1110538390 sf1110532935 11 10538390 1.46E-09 6.97E-07
vg0527800724 sf0527738081 5 27800724 2.61E-08 2.64E-06
vg0205781493 sf0205781493 2 5781493 3.31E-08 3.37E-06
vg0134987787 sf0134986744 1 34987787 4.63E-08 NA
vg0709880588 sf0709879594 7 9880588 5.09E-08 1.08E-06
vg1106408812 sf1106404564 11 6408812 6.65E-08 NA
vg0918725272 sf0918724272 9 18725272 7.12E-08 1.49E-06
vg0204231982 sf0204231979 2 4231982 8.97E-08 2.56E-06
vg0816111876 sf0816109162 8 16111876 NA 1.09E-06
vg0235561608 sf0235555739 2 35561608 NA 1.12E-06
vg0816069844 sf0816067130 8 16069844 NA 1.15E-06
vg0318242792 sf0318241574 3 18242792 NA 1.31E-06
vg0311647322 sf0311646040 3 11647322 NA 1.36E-06
vg0327574120 sf0327567173 3 27574120 NA 1.41E-06
vg0810997379 sf0810996384 8 10997379 NA 1.47E-06
vg0821683762 sf0821681049 8 21683762 NA 1.85E-06
vg1215937004 sf1215934300 12 15937004 NA 2.77E-06
vg0102501634 sf0102500634 1 2501634 NA 2.81E-06
vg0101491555 sf0101490555 1 1491555 NA 2.98E-06
vg1011813560 sf1011742375 10 11813560 NA 3.90E-06
vg0720597280 sf0720596287 7 20597280 NA 4.35E-06
vg0519717196 sf0519654680 5 19717196 NA 4.54E-06