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 mr1952 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
vg0501779982 sf0501779965 5 1779982 4.09E-11 1.73E-07
vg0502188071 sf0502188046 5 2188071 2.49E-09 3.75E-07
vg0328876399 sf0328869452 3 28876399 3.20E-08 6.05E-06
vg0420718113 sf0420546156 4 20718113 5.93E-08 4.13E-06
vg0431931212 sf0431746107 4 31931212 8.80E-08 NA
vg0709672527 sf0709671533 7 9672527 8.11E-07 2.38E-06
vg0709673627 sf0709672633 7 9673627 8.29E-07 1.79E-06
vg0421352088 sf0421180142 4 21352088 1.52E-06 3.23E-06
vg0205968700 sf0205968700 2 5968700 7.08E-06 3.60E-06
vg0421020772 sf0420848825 4 21020772 NA 7.03E-07