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 mr1250 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
vg0217639783 sf0217633913 2 17639783 3.89E-10 2.19E-06
vg0222145560 sf0222139691 2 22145560 4.11E-10 NA
vg0212570411 sf0212570407 2 12570411 4.90E-10 NA
vg1125221707 sf1124755547 11 25221707 7.28E-10 NA
vg0620481199 sf0620480202 6 20481199 7.49E-10 NA
vg0422772120 sf0422587003 4 22772120 3.63E-07 2.43E-06
vg0308205423 sf0308204361 3 8205423 5.35E-07 NA