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 mr1515 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
vg0325710457 sf0325708475 3 25710457 1.94E-15 1.04E-11
vg0525124226 sf0525061641 5 25124226 6.75E-10 1.40E-06
vg1121711093 sf1121244970 11 21711093 1.63E-09 8.66E-06
vg1002824620 sf1002823597 10 2824620 3.88E-09 8.78E-06
vg0317495339 sf0317494121 3 17495339 5.92E-09 NA
vg0202731072 sf0202731070 2 2731072 2.44E-08 1.10E-06
vg0711956530 sf0711955536 7 11956530 4.88E-08 2.46E-06
vg0727691010 sf0727690017 7 27691010 7.16E-07 2.73E-06
vg0225789722 sf0225783853 2 25789722 1.15E-06 1.98E-06
vg1006612280 sf1006627903 10 6612280 NA 5.81E-06