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 mr1215 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
vg0610144953 sf0610143954 6 10144953 4.13E-13 1.63E-09
vg0610463539 sf0610462540 6 10463539 4.66E-08 1.16E-06
vg0623833223 sf0623832226 6 23833223 1.22E-06 1.97E-06
vg0726257978 sf0726256984 7 26257978 NA 7.79E-07
vg0809369523 sf0809368527 8 9369523 NA 2.85E-06
vg0403330366 sf0403325969 4 3330366 NA 3.96E-06
vg0403330359 sf0403325962 4 3330359 NA 4.37E-06