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 mr1811 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
vg0102103204 sf0102102204 1 2103204 1.68E-08 3.55E-06
vg0132988931 sf0132987887 1 32988931 2.74E-08 NA
vg0335297514 sf0335290383 3 35297514 5.66E-08 5.30E-06
vg0902107236 sf0902106236 9 2107236 2.79E-07 2.80E-06
vg1215307750 sf1215305048 12 15307750 8.52E-07 1.29E-06
vg0113652030 sf0113651004 1 13652030 4.33E-06 8.81E-07
vg1207840077 sf1207837483 12 7840077 6.17E-06 2.17E-06
vg0621412586 sf0621411589 6 21412586 NA 3.30E-06