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 mr1418 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
vg1124252852 sf1123786722 11 24252852 3.25E-07 3.25E-07
vg0335281661 sf0335274530 3 35281661 8.98E-07 8.99E-07
vg0223518691 sf0223512822 2 23518691 1.30E-06 1.30E-06
vg0509233251 sf0509233180 5 9233251 1.36E-06 1.36E-06
vg0324965295 sf0324963375 3 24965295 2.03E-06 2.03E-06
vg0915815139 sf0915814138 9 15815139 2.11E-06 2.11E-06
vg0223522948 sf0223517079 2 23522948 2.26E-06 2.26E-06
vg0223074046 sf0223068177 2 23074046 3.04E-06 3.04E-06
vg1011340145 sf1011268965 10 11340145 3.27E-06 3.27E-06
vg0314986971 sf0314985618 3 14986971 3.33E-06 3.34E-06
vg0901298010 sf0901297010 9 1298010 3.36E-06 3.36E-06
vg1001343441 sf1001342418 10 1343441 3.50E-06 3.50E-06
vg0816086900 sf0816084186 8 16086900 3.84E-06 3.84E-06
vg0805900956 sf0805899959 8 5900956 4.35E-06 4.36E-06
vg0223170147 sf0223164278 2 23170147 4.38E-06 4.38E-06
vg1214703763 sf1214701104 12 14703763 4.59E-06 4.59E-06