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 mr1497 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
vg0235013338 sf0235007469 2 35013338 3.31E-09 NA
vg1105571587 sf1105567339 11 5571587 5.63E-09 NA
vg0406498165 sf0406493608 4 6498165 6.41E-08 NA
vg0103644963 sf0103643963 1 3644963 7.48E-08 NA
vg1103059501 sf1103055405 11 3059501 7.67E-08 NA
vg0526092128 sf0526029548 5 26092128 4.10E-07 NA
vg1208526343 sf1208523750 12 8526343 9.74E-06 NA
vg0308275054 sf0308273992 3 8275054 NA 5.82E-06