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 mr1147 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
vg0719140447 sf0719139454 7 19140447 5.28E-17 NA
vg0305023781 sf0305022783 3 5023781 7.74E-17 4.20E-06
vg0305033955 sf0305032957 3 5033955 1.15E-16 7.57E-06
vg0707583684 sf0707582689 7 7583684 1.69E-16 8.25E-06
vg1017949223 sf1017877995 10 17949223 3.15E-16 NA
vg0401723023 sf0401718572 4 1723023 3.76E-16 NA
vg0525802961 sf0525740382 5 25802961 2.71E-14 NA
vg1009321613 sf1009250434 10 9321613 3.24E-14 6.23E-08
vg0412457585 sf0412448300 4 12457585 1.27E-13 2.82E-07
vg0401720392 sf0401715941 4 1720392 3.80E-13 2.34E-06
vg0518984986 sf0518922470 5 18984986 NA 1.32E-06
vg1006456883 sf1006472506 10 6456883 NA 1.49E-06
vg1009450795 sf1009379616 10 9450795 NA 1.62E-06
vg0916030541 sf0916029540 9 16030541 NA 2.38E-06
vg1214678248 sf1214675587 12 14678248 NA 3.88E-06