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 mr1361 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
vg1018726980 sf1018655537 10 18726980 1.33E-18 6.95E-07
vg0113976407 sf0113975381 1 13976407 3.48E-17 NA
vg0504766271 sf0504766248 5 4766271 3.97E-17 NA
vg1219113826 sf1219085262 12 19113826 4.49E-17 NA
vg1113912544 sf1113448865 11 13912544 5.64E-17 2.14E-06
vg1109924691 sf1109919268 11 9924691 4.52E-14 NA
vg0502220853 sf0502220828 5 2220853 NA 1.07E-06
vg1218866013 sf1218837448 12 18866013 NA 2.16E-06