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 mr1360 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
vg1103571301 sf1103567204 11 3571301 3.69E-12 NA
vg0124036172 sf0124035128 1 24036172 5.36E-11 NA
vg0726949432 sf0726948438 7 26949432 2.31E-10 NA
vg0726949917 sf0726948923 7 26949917 3.13E-10 3.66E-06
vg0139588846 sf0139587803 1 39588846 3.31E-10 NA
vg0726932441 sf0726931447 7 26932441 3.75E-10 NA
vg1113075743 sf1112612064 11 13075743 7.18E-08 5.08E-07
vg0224679293 sf0224673424 2 24679293 1.32E-06 NA
vg0306409520 sf0306408520 3 6409520 2.21E-06 NA
vg1217915504 sf1217886938 12 17915504 4.02E-06 NA
vg1003433058 sf1003432035 10 3433058 5.85E-06 4.24E-07
vg0412734026 sf0412724736 4 12734026 8.99E-06 1.65E-06
vg0501022850 sf0501022834 5 1022850 NA 8.86E-07
vg0224550937 sf0224545068 2 24550937 NA 1.85E-06
vg0107647091 sf0107646091 1 7647091 NA 3.20E-06
vg0500699493 sf0500699493 5 699493 NA 8.33E-06