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 mr1490 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
vg1215977007 sf1215974303 12 15977007 1.10E-205 3.03E-73
vg1215968758 sf1215966054 12 15968758 3.86E-199 2.76E-73
vg1210219854 sf1210217266 12 10219854 1.87E-96 8.38E-06
vg1224007541 sf1223973994 12 24007541 3.03E-85 NA
vg0217066401 sf0217060531 2 17066401 7.17E-78 NA
vg1213439429 sf1213436767 12 13439429 1.94E-75 NA
vg1215992116 sf1215989412 12 15992116 NA 3.14E-33
vg1215969757 sf1215967053 12 15969757 NA 6.21E-18
vg1216151755 sf1216149051 12 16151755 NA 1.13E-13
vg1217327067 sf1217321022 12 17327067 NA 5.20E-13
vg1216532835 sf1216530128 12 16532835 NA 3.49E-11
vg1216320605 sf1216317901 12 16320605 NA 1.25E-10
vg1215321806 sf1215319104 12 15321806 NA 8.56E-10
vg0610620315 sf0610619316 6 10620315 NA 1.33E-09
vg1215893630 sf1215890926 12 15893630 NA 1.67E-09
vg1216413575 sf1216410868 12 16413575 NA 1.86E-09
vg1216545702 sf1216542995 12 16545702 NA 3.22E-09
vg1216470015 sf1216467308 12 16470015 NA 5.15E-09
vg1215763538 sf1215760835 12 15763538 NA 1.10E-08
vg1215962650 sf1215959946 12 15962650 NA 1.35E-08
vg1216550375 sf1216547668 12 16550375 NA 2.31E-08
vg1216345935 sf1216343231 12 16345935 NA 2.74E-08
vg1216346285 sf1216343581 12 16346285 NA 3.28E-08
vg1216257098 sf1216254394 12 16257098 NA 6.99E-08
vg1214879927 sf1214877268 12 14879927 NA 7.18E-08
vg0920348485 sf0920348004 9 20348485 NA 1.06E-07
vg1117717695 sf1117251551 11 17717695 NA 1.17E-07
vg1216165822 sf1216163118 12 16165822 NA 1.60E-07
vg1215780845 sf1215778142 12 15780845 NA 1.82E-07
vg0408410897 sf0408406171 4 8410897 NA 4.60E-07
vg1207786635 sf1207784041 12 7786635 NA 7.48E-06