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 mr1918 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
vg1108581599 sf1108576209 11 8581599 5.79E-08 5.79E-08
vg0221478143 sf0221472274 2 21478143 7.85E-08 7.85E-08
vg0221520232 sf0221514363 2 21520232 7.85E-08 7.85E-08
vg0500894385 sf0500894367 5 894385 3.21E-07 3.22E-07
vg0621552663 sf0621551666 6 21552663 3.37E-07 3.37E-07
vg1108111928 sf1108107673 11 8111928 8.86E-07 8.86E-07
vg0222833455 sf0222827586 2 22833455 1.08E-06 1.08E-06
vg1107498561 sf1107494306 11 7498561 1.19E-06 1.19E-06
vg0135058637 sf0135057594 1 35058637 1.60E-06 1.60E-06
vg1222586644 sf1222553083 12 22586644 2.14E-06 2.14E-06
vg1105847289 sf1105843041 11 5847289 2.24E-06 2.24E-06
vg0320967721 sf0320966231 3 20967721 2.60E-06 2.60E-06
vg0232851006 sf0232845137 2 32851006 4.09E-06 4.09E-06
vg0816229664 sf0816226950 8 16229664 4.43E-06 4.43E-06
vg1122413063 sf1121946934 11 22413063 4.90E-06 4.90E-06