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 mr1192 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
vg1213218383 sf1213215721 12 13218383 2.11E-08 2.12E-08
vg0726559137 sf0726558143 7 26559137 1.36E-07 1.36E-07
vg0223525077 sf0223519208 2 23525077 5.34E-07 5.34E-07
vg0808428148 sf0808427152 8 8428148 1.54E-06 1.54E-06
vg0516498972 sf0516441454 5 16498972 1.60E-06 1.61E-06
vg0907912674 sf0907911674 9 7912674 2.39E-06 2.39E-06
vg0427421479 sf0427236343 4 27421479 4.65E-06 4.66E-06