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 mr1209 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
vg0431655631 sf0431470524 4 31655631 2.97E-08 2.97E-08
vg1104979071 sf1104974882 11 4979071 3.07E-07 3.08E-07
vg1104978992 sf1104974803 11 4978992 3.10E-07 3.10E-07
vg1124303443 sf1123837313 11 24303443 3.63E-07 3.63E-07
vg0726847020 sf0726846026 7 26847020 7.45E-07 7.45E-07
vg0300249514 sf0300248514 3 249514 1.30E-06 1.30E-06
vg1106375766 sf1106371518 11 6375766 1.57E-06 1.57E-06
vg0823213341 sf0823210628 8 23213341 1.63E-06 1.63E-06
vg0130290451 sf0130289406 1 30290451 1.89E-06 1.89E-06
vg0318751668 sf0318750428 3 18751668 2.01E-06 2.01E-06
vg0125460828 sf0125459784 1 25460828 3.13E-06 3.14E-06
vg1214822308 sf1214819649 12 14822308 3.26E-06 3.26E-06
vg0200505558 sf0200505558 2 505558 3.99E-06 3.99E-06
vg0514011016 sf0513953560 5 14011016 4.16E-06 4.16E-06
vg0710432728 sf0710431734 7 10432728 4.81E-06 4.81E-06
vg1207456492 sf1207453898 12 7456492 4.98E-06 4.98E-06