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 mr1265 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
vg0716080501 sf0716079508 7 16080501 1.92E-14 4.14E-15
vg0716085095 sf0716084102 7 16085095 2.90E-14 6.77E-15
vg0716085423 sf0716084430 7 16085423 3.86E-14 3.60E-15
vg1207608413 sf1207605818 12 7608413 2.90E-12 NA
vg1102946444 sf1102942348 11 2946444 5.02E-12 NA
vg0827750460 sf0827747746 8 27750460 1.20E-11 6.09E-06
vg1207623062 sf1207620464 12 7623062 3.85E-11 NA
vg0141773367 sf0141772324 1 41773367 9.81E-11 NA
vg1117476840 sf1117010695 11 17476840 1.16E-07 4.72E-07
vg1117565966 sf1117099822 11 17565966 3.45E-07 NA
vg1002102834 sf1002101811 10 2102834 1.09E-06 3.06E-06
vg0224699387 sf0224693518 2 24699387 1.36E-06 9.43E-07
vg0400301685 sf0400300685 4 301685 1.42E-06 3.93E-07
vg0722387380 sf0722386387 7 22387380 1.79E-06 2.15E-06
vg0220941121 sf0220935253 2 20941121 3.22E-06 3.93E-06
vg0714860463 sf0714859470 7 14860463 NA 4.48E-08
vg0716100570 sf0716099577 7 16100570 NA 1.68E-06
vg0716418454 sf0716417461 7 16418454 NA 4.43E-06