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
vg1117584893 sf1117118750 11 17584893 6.94E-10 1.44E-07
vg0125082187 sf0125081143 1 25082187 3.00E-07 2.98E-06
vg0623833223 sf0623832226 6 23833223 9.77E-07 9.05E-07
vg0504650681 sf0504650658 5 4650681 1.84E-06 1.97E-06
vg0920044521 sf0920044040 9 20044521 2.86E-06 2.70E-06
vg0701484527 sf0701483527 7 1484527 4.29E-06 2.57E-06
vg0140594988 sf0140593945 1 40594988 6.47E-06 NA
vg0714405504 sf0714404511 7 14405504 NA 3.81E-06