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 mr1583 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
vg1217218651 sf1217212606 12 17218651 1.31E-12 5.18E-08
vg0506207863 sf0506207802 5 6207863 1.56E-12 1.78E-07
vg0609657256 sf0609656257 6 9657256 1.74E-12 6.65E-08
vg0814545221 sf0814542507 8 14545221 1.83E-12 8.05E-07
vg0502976477 sf0502976453 5 2976477 1.18E-11 1.12E-06
vg1104144721 sf1104140623 11 4144721 1.24E-11 1.00E-06
vg0204744487 sf0204744484 2 4744487 1.84E-11 1.23E-06
vg1002115213 sf1002114190 10 2115213 3.21E-11 7.49E-07
vg0911981636 sf0911980635 9 11981636 4.98E-11 3.96E-07
vg0624696649 sf0624695652 6 24696649 5.24E-11 9.54E-07
vg0527177720 sf0527115076 5 27177720 6.44E-11 1.75E-06
vg1215688513 sf1215685810 12 15688513 1.08E-10 1.41E-07
vg0811614155 sf0811613160 8 11614155 1.52E-10 2.32E-06
vg1125440253 sf1124974092 11 25440253 3.10E-10 3.77E-06
vg0506412273 sf0506412212 5 6412273 6.23E-10 2.84E-06
vg0728023162 sf0728022169 7 28023162 8.47E-10 1.67E-06
vg0229110646 sf0229104777 2 29110646 8.92E-10 1.15E-06
vg1117628825 sf1117162681 11 17628825 3.17E-08 6.02E-07
vg0604647765 sf0604646766 6 4647765 1.45E-06 NA