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 mr1154 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
vg0619603076 sf0619602079 6 19603076 5.71E-57 NA
vg0626042276 sf0626041279 6 26042276 5.78E-57 NA
vg0917214543 sf0917213542 9 17214543 8.28E-57 NA
vg0211534075 sf0211534071 2 11534075 1.62E-56 NA
vg0215681856 sf0215675986 2 15681856 5.49E-56 NA
vg0130732040 sf0130730996 1 30732040 NA 3.98E-12
vg0130670983 sf0130669939 1 30670983 NA 4.35E-12
vg0130644853 sf0130643809 1 30644853 NA 4.80E-09
vg1115413712 sf1114950024 11 15413712 NA 2.92E-07
vg0303180062 sf0303179058 3 3180062 NA 6.01E-07
vg0303169957 sf0303168953 3 3169957 NA 8.30E-07
vg0135794714 sf0135793671 1 35794714 NA 9.18E-07
vg0139977615 sf0139976572 1 39977615 NA 1.18E-06
vg0129917132 sf0129916087 1 29917132 NA 2.57E-06
vg0134539333 sf0134538290 1 34539333 NA 3.29E-06
vg0138627461 sf0138626418 1 38627461 NA 4.08E-06