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 mr1901 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
vg0217567846 sf0217561976 2 17567846 8.58E-10 5.81E-08
vg1113004581 sf1112540902 11 13004581 2.39E-08 5.02E-06
vg0214797114 sf0214791244 2 14797114 2.41E-08 5.26E-07
vg0217105238 sf0217099368 2 17105238 6.37E-08 6.37E-08
vg0132938909 sf0132937865 1 32938909 1.66E-07 1.43E-06
vg0210605172 sf0210605170 2 10605172 3.24E-06 1.85E-06
vg1104324598 sf1104320500 11 4324598 7.63E-06 3.70E-06
vg0319922800 sf0319921311 3 19922800 9.06E-06 2.21E-06
vg0132937128 sf0132936084 1 32937128 NA 1.09E-06
vg0713886934 sf0713885941 7 13886934 NA 4.49E-06