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 mr1411 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
vg0719049906 sf0719048913 7 19049906 4.69E-44 3.28E-32
vg1100987581 sf1100986582 11 987581 2.00E-31 NA
vg0315196176 sf0315194823 3 15196176 1.58E-30 8.65E-07
vg0215716465 sf0215710595 2 15716465 2.35E-30 NA
vg0608633240 sf0608632241 6 8633240 1.31E-29 NA
vg0315290362 sf0315289009 3 15290362 3.75E-28 1.71E-08
vg0719055344 sf0719054351 7 19055344 NA 1.12E-20
vg0719323752 sf0719322759 7 19323752 NA 3.40E-20
vg0719091461 sf0719090468 7 19091461 NA 8.18E-17
vg0719140498 sf0719139505 7 19140498 NA 3.54E-16
vg0719064944 sf0719063951 7 19064944 NA 1.42E-12
vg0421592157 sf0421420207 4 21592157 NA 1.80E-11
vg0909775480 sf0909774479 9 9775480 NA 2.70E-11
vg0329561125 sf0329554165 3 29561125 NA 4.64E-11
vg0428494128 sf0428308982 4 28494128 NA 6.70E-11
vg0625211382 sf0625210385 6 25211382 NA 1.32E-10
vg1105544417 sf1105540169 11 5544417 NA 3.25E-10
vg0719466615 sf0719465622 7 19466615 NA 4.53E-10
vg0816446429 sf0816443715 8 16446429 NA 4.88E-10
vg0707699197 sf0707698202 7 7699197 NA 2.67E-09
vg0720529894 sf0720528901 7 20529894 NA 1.32E-08
vg0136510873 sf0136509830 1 36510873 NA 3.07E-08
vg0901040131 sf0901039131 9 1040131 NA 4.50E-08
vg0113087370 sf0113086344 1 13087370 NA 4.80E-08
vg0620744993 sf0620743996 6 20744993 NA 5.76E-08
vg0719436399 sf0719435406 7 19436399 NA 7.91E-08
vg0708152905 sf0708151910 7 8152905 NA 8.18E-08
vg0714249785 sf0714248792 7 14249785 NA 1.37E-07
vg0315200001 sf0315198648 3 15200001 NA 2.35E-07