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 mr1882 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
vg0314128657 sf0314127346 3 14128657 1.30E-09 1.28E-06
vg1207399610 sf1207397017 12 7399610 3.95E-09 NA
vg0141705283 sf0141704240 1 41705283 5.55E-09 NA
vg0726932441 sf0726931447 7 26932441 1.62E-08 NA
vg0406464034 sf0406459477 4 6464034 2.16E-08 NA
vg0713275136 sf0713274143 7 13275136 6.90E-08 1.76E-06
vg0404438776 sf0404434380 4 4438776 7.62E-08 NA
vg0406472365 sf0406467808 4 6472365 7.91E-08 1.34E-06
vg0907680153 sf0907679153 9 7680153 1.05E-07 1.57E-06
vg1100321101 sf1100320103 11 321101 5.40E-06 NA
vg0406877172 sf0406872617 4 6877172 NA 3.05E-06