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 mr1083 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
vg0719001862 sf0719000869 7 19001862 1.36E-34 5.67E-14
vg0305696086 sf0305695086 3 5696086 6.81E-30 5.12E-09
vg0704296812 sf0704295813 7 4296812 7.64E-30 1.22E-09
vg0612905536 sf0612904537 6 12905536 6.35E-29 2.27E-06
vg0708204553 sf0708203558 7 8204553 6.76E-29 2.43E-09
vg0719049906 sf0719048913 7 19049906 4.15E-28 1.95E-22
vg0215999292 sf0215993422 2 15999292 1.58E-25 1.47E-11
vg0305138684 sf0305137686 3 5138684 2.07E-24 1.06E-11
vg0220550093 sf0220544225 2 20550093 2.96E-24 1.21E-08
vg0719091461 sf0719090468 7 19091461 NA 3.48E-21
vg0719140498 sf0719139505 7 19140498 NA 3.59E-16
vg0719055344 sf0719054351 7 19055344 NA 8.55E-13
vg0719067465 sf0719066472 7 19067465 NA 3.48E-11
vg0721053259 sf0721052266 7 21053259 NA 3.59E-11
vg0719730010 sf0719729017 7 19730010 NA 4.86E-11
vg1217507757 sf1217501712 12 17507757 NA 7.30E-11
vg0719466615 sf0719465622 7 19466615 NA 1.58E-10
vg1128595453 sf1128072232 11 28595453 NA 2.33E-10
vg1204022544 sf1204021532 12 4022544 NA 3.56E-10
vg0707667722 sf0707666727 7 7667722 NA 4.92E-10
vg0428494128 sf0428308982 4 28494128 NA 1.82E-09
vg0113087370 sf0113086344 1 13087370 NA 3.05E-09
vg0719150237 sf0719149244 7 19150237 NA 4.62E-09
vg1122928318 sf1122462189 11 22928318 NA 5.55E-09
vg0617705132 sf0617704135 6 17705132 NA 1.01E-08
vg0711927385 sf0711926391 7 11927385 NA 5.03E-07
vg1212214384 sf1212211722 12 12214384 NA 9.39E-06