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 mr1672 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
vg0137961753 sf0137960710 1 37961753 5.31E-121 6.66E-25
vg1119486642 sf1119020330 11 19486642 2.04E-99 3.01E-08
vg0107143963 sf0107142963 1 7143963 9.55E-95 NA
vg1116523467 sf1116058344 11 16523467 2.17E-92 3.11E-06
vg0313856584 sf0313855301 3 13856584 1.33E-91 NA
vg0111793207 sf0111792181 1 11793207 6.88E-90 1.65E-06
vg1116975128 sf1116508969 11 16975128 1.87E-89 2.65E-07
vg0811308449 sf0811307454 8 11308449 5.38E-86 7.83E-07
vg0400468558 sf0400467556 4 468558 NA 2.77E-10
vg0400388457 sf0400387455 4 388457 NA 4.85E-10
vg0917927607 sf0917926606 9 17927607 NA 2.20E-08
vg0400397491 sf0400396489 4 397491 NA 2.94E-08
vg0400014283 sf0400013283 4 14283 NA 5.31E-08
vg0108147243 sf0108146243 1 8147243 NA 3.79E-07
vg1107129860 sf1107125605 11 7129860 NA 1.01E-06
vg0613618219 sf0613617220 6 13618219 NA 1.17E-06
vg0400357479 sf0400356479 4 357479 NA 1.40E-06
vg0123465245 sf0123464201 1 23465245 NA 1.43E-06
vg0907797330 sf0907796330 9 7797330 NA 1.81E-06
vg1106330395 sf1106326147 11 6330395 NA 1.89E-06
vg0628049668 sf0628048670 6 28049668 NA 2.04E-06
vg0224598014 sf0224592145 2 24598014 NA 2.24E-06
vg0700016965 sf0700015965 7 16965 NA 2.25E-06
vg0140632361 sf0140631318 1 40632361 NA 2.48E-06
vg0802773819 sf0802772822 8 2773819 NA 5.09E-06