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 mr1437 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 2.03E-70 4.64E-33
vg0305665264 sf0305664264 3 5665264 5.61E-53 NA
vg0917918788 sf0917917787 9 17918788 2.80E-51 NA
vg0706847379 sf0706846384 7 6847379 4.72E-51 NA
vg0504619344 sf0504619321 5 4619344 5.67E-51 NA
vg0626897338 sf0626896341 6 26897338 5.23E-46 4.76E-07
vg0719091461 sf0719090468 7 19091461 NA 2.78E-24
vg0719200639 sf0719199646 7 19200639 NA 4.10E-20
vg0719188413 sf0719187420 7 19188413 NA 1.17E-13
vg0719060385 sf0719059392 7 19060385 NA 7.60E-13
vg0718985745 sf0718984752 7 18985745 NA 7.77E-11
vg0719067465 sf0719066472 7 19067465 NA 1.34E-10
vg0719431865 sf0719430872 7 19431865 NA 2.60E-10
vg0719618102 sf0719617109 7 19618102 NA 4.15E-09
vg0315309690 sf0315308337 3 15309690 NA 1.81E-08
vg0828401472 sf0828398758 8 28401472 NA 6.11E-08
vg0719466615 sf0719465622 7 19466615 NA 6.39E-08
vg0617336375 sf0617335378 6 17336375 NA 1.06E-07
vg0705591916 sf0705590917 7 5591916 NA 2.74E-07
vg0113087370 sf0113086344 1 13087370 NA 7.67E-07
vg0901628621 sf0901627621 9 1628621 NA 9.23E-07
vg0302581223 sf0302580219 3 2581223 NA 9.60E-07
vg0718922665 sf0718921672 7 18922665 NA 1.14E-06
vg1002954217 sf1002953194 10 2954217 NA 1.34E-06
vg0813135425 sf0813132985 8 13135425 NA 1.38E-06
vg0722026351 sf0722025358 7 22026351 NA 1.57E-06
vg0719223576 sf0719222583 7 19223576 NA 1.72E-06
vg0515005729 sf0514948272 5 15005729 NA 1.84E-06
vg0708714403 sf0708713408 7 8714403 NA 1.89E-06