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 mr1514 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
vg0507006907 sf0507006849 5 7006907 3.24E-24 2.82E-11
vg0506870350 sf0506870292 5 6870350 7.07E-22 7.19E-13
vg0506869876 sf0506869818 5 6869876 1.88E-19 6.36E-12
vg0506870338 sf0506870280 5 6870338 8.14E-19 5.01E-12
vg0229036658 sf0229030789 2 29036658 8.96E-18 9.34E-06
vg0327449535 sf0327442588 3 27449535 1.17E-16 NA
vg0229375522 sf0229369653 2 29375522 1.48E-16 9.98E-07
vg1109538933 sf1109533510 11 9538933 4.95E-16 1.49E-07
vg0203405625 sf0203405623 2 3405625 9.30E-14 7.13E-10
vg0508342418 sf0508342346 5 8342418 NA 9.25E-08
vg0511756975 sf0511756905 5 11756975 NA 1.09E-07
vg1009362967 sf1009291788 10 9362967 NA 1.23E-07
vg1001247140 sf1001246117 10 1247140 NA 4.84E-07
vg0509203069 sf0509202998 5 9203069 NA 1.17E-06
vg0100483172 sf0100482172 1 483172 NA 1.68E-06
vg0514716289 sf0514658832 5 14716289 NA 3.58E-06