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 mr1103 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 1.24E-100 4.07E-53
vg0719199004 sf0719198011 7 19199004 1.89E-94 1.44E-47
vg0917918788 sf0917917787 9 17918788 6.45E-79 NA
vg0305665264 sf0305664264 3 5665264 2.77E-75 NA
vg0626853373 sf0626852376 6 26853373 3.16E-75 4.12E-07
vg0706732370 sf0706731375 7 6732370 5.74E-75 NA
vg0626897338 sf0626896341 6 26897338 2.85E-74 3.72E-09
vg0719091461 sf0719090468 7 19091461 NA 7.81E-41
vg0719055344 sf0719054351 7 19055344 NA 3.76E-35
vg0719145578 sf0719144585 7 19145578 NA 7.07E-19
vg0719466615 sf0719465622 7 19466615 NA 3.20E-15
vg0719067465 sf0719066472 7 19067465 NA 1.07E-14
vg0707699197 sf0707698202 7 7699197 NA 3.82E-12
vg0719618102 sf0719617109 7 19618102 NA 1.62E-11
vg0719436399 sf0719435406 7 19436399 NA 3.55E-11
vg0718985745 sf0718984752 7 18985745 NA 8.06E-11
vg0828401472 sf0828398758 8 28401472 NA 1.11E-10
vg0113087370 sf0113086344 1 13087370 NA 1.94E-10
vg0408294186 sf0408289460 4 8294186 NA 1.41E-09
vg0302581223 sf0302580219 3 2581223 NA 2.14E-09
vg0909775480 sf0909774479 9 9775480 NA 2.62E-09
vg1105544417 sf1105540169 11 5544417 NA 2.77E-09
vg0719452729 sf0719451736 7 19452729 NA 6.76E-09
vg0617336375 sf0617335378 6 17336375 NA 8.76E-09
vg0329561125 sf0329554165 3 29561125 NA 9.38E-09
vg0828393303 sf0828390589 8 28393303 NA 1.15E-08
vg0719064343 sf0719063350 7 19064343 NA 1.19E-08
vg0127881125 sf0127880081 1 27881125 NA 1.23E-08
vg0810479074 sf0810478078 8 10479074 NA 4.03E-07
vg0127893586 sf0127892542 1 27893586 NA 9.09E-07