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 mr1252 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
vg0414127903 sf0414118618 4 14127903 4.68E-10 NA
vg0234326223 sf0234320354 2 34326223 8.67E-10 NA
vg0520045994 sf0519983470 5 20045994 8.99E-10 NA
vg0132936369 sf0132935325 1 32936369 9.40E-10 NA
vg0524852282 sf0524789697 5 24852282 1.03E-09 NA
vg0421834990 sf0421663040 4 21834990 2.50E-08 2.02E-06
vg1220025663 sf1219997105 12 20025663 4.91E-08 NA
vg0203965753 sf0203965750 2 3965753 1.89E-07 NA
vg0327596758 sf0327589811 3 27596758 5.92E-07 1.27E-06
vg0325734436 sf0325732454 3 25734436 1.28E-06 9.24E-08
vg0130750236 sf0130749192 1 30750236 NA 1.62E-06