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 mr1064 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
vg0625163806 sf0625162809 6 25163806 3.05E-66 NA
vg0915747582 sf0915746581 9 15747582 2.50E-65 NA
vg0313637100 sf0313635817 3 13637100 1.89E-64 NA
vg0922789940 sf0922789459 9 22789940 6.20E-64 NA
vg0617880328 sf0617879331 6 17880328 3.70E-63 NA
vg0626699518 sf0626698521 6 26699518 1.56E-61 7.16E-09
vg0430559445 sf0430374320 4 30559445 NA 9.79E-16
vg0430475778 sf0430290656 4 30475778 NA 3.49E-10
vg0430612645 sf0430427520 4 30612645 NA 8.46E-09
vg0821270765 sf0821268052 8 21270765 NA 1.43E-07
vg0430478309 sf0430293187 4 30478309 NA 1.59E-07
vg0623884291 sf0623883294 6 23884291 NA 3.96E-07
vg0523302726 sf0523240147 5 23302726 NA 4.88E-07
vg0707315648 sf0707314653 7 7315648 NA 6.17E-07
vg0307775185 sf0307774123 3 7775185 NA 9.76E-07
vg0217111661 sf0217105791 2 17111661 NA 1.27E-06
vg1214390025 sf1214387366 12 14390025 NA 1.32E-06
vg0707353401 sf0707352406 7 7353401 NA 2.21E-06
vg0223115199 sf0223109330 2 23115199 NA 2.30E-06
vg0430677343 sf0430492218 4 30677343 NA 2.69E-06
vg1022646939 sf1022575413 10 22646939 NA 3.19E-06
vg0315818553 sf0315817200 3 15818553 NA 4.65E-06
vg0138577662 sf0138576619 1 38577662 NA 7.09E-06