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 mr1851 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
vg0419247022 sf0419075060 4 19247022 8.86E-21 3.11E-11
vg0306769175 sf0306768175 3 6769175 1.34E-16 8.20E-07
vg0202200150 sf0202200150 2 2200150 6.86E-16 NA
vg0919319021 sf0919318611 9 19319021 1.57E-15 NA
vg0310902932 sf0310901650 3 10902932 1.79E-15 5.40E-06
vg0808663101 sf0808662105 8 8663101 2.01E-13 1.44E-06
vg0500918476 sf0500918459 5 918476 4.71E-13 1.94E-07
vg1221167547 sf1221134093 12 21167547 2.31E-12 3.72E-06
vg0124418254 sf0124417210 1 24418254 1.16E-11 3.17E-07
vg1103050384 sf1103046288 11 3050384 2.11E-10 NA
vg0219786354 sf0219780486 2 19786354 9.90E-10 2.30E-06
vg0626066579 sf0626065582 6 26066579 NA 5.31E-07
vg1223866012 sf1223832465 12 23866012 NA 1.42E-06
vg0827295276 sf0827292562 8 27295276 NA 1.46E-06
vg0124427686 sf0124426642 1 24427686 NA 1.76E-06
vg0819180192 sf0819177479 8 19180192 NA 1.77E-06
vg0622788757 sf0622787760 6 22788757 NA 2.04E-06
vg0517977616 sf0517917102 5 17977616 NA 4.73E-06