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 mr1827 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
vg0518026034 sf0517965520 5 18026034 1.84E-13 4.33E-07
vg0518072547 sf0518012033 5 18072547 1.98E-13 3.59E-07
vg0803470128 sf0803469131 8 3470128 2.02E-12 8.68E-06
vg0804298332 sf0804297335 8 4298332 2.92E-12 1.31E-06
vg0528270837 sf0528208192 5 28270837 4.24E-12 NA
vg1119035040 sf1118568728 11 19035040 1.32E-11 NA
vg0329444805 sf0329437845 3 29444805 3.58E-11 NA
vg1012456399 sf1012385214 10 12456399 1.82E-08 1.97E-06
vg1012720747 sf1012649562 10 12720747 NA 8.04E-06