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 mr1302 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
vg0822105767 sf0822103054 8 22105767 5.23E-12 7.16E-06
vg0130364087 sf0130363043 1 30364087 1.15E-11 NA
vg0823144488 sf0823141775 8 23144488 3.09E-11 NA
vg1102430558 sf1102426462 11 2430558 3.38E-11 9.07E-06
vg0721356842 sf0721355849 7 21356842 5.69E-11 NA
vg0434822396 sf0434637287 4 34822396 9.20E-10 NA
vg0127027223 sf0127026179 1 27027223 6.21E-09 1.79E-06
vg0906631032 sf0906630032 9 6631032 9.40E-09 1.39E-06
vg0400137046 sf0400136046 4 137046 NA 6.61E-07
vg0431515534 sf0431330433 4 31515534 NA 2.89E-06
vg1214822308 sf1214819649 12 14822308 NA 4.45E-06
vg0820479378 sf0820476665 8 20479378 NA 4.92E-06