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 mr1577 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
vg1215970970 sf1215968266 12 15970970 8.88E-09 1.15E-08
vg1218115012 sf1218086448 12 18115012 3.21E-08 1.61E-06
vg1014019485 sf1013948251 10 14019485 6.12E-08 2.84E-06
vg1215427937 sf1215425235 12 15427937 1.53E-07 1.57E-06
vg1209353508 sf1209350917 12 9353508 1.88E-07 9.62E-08
vg0610852428 sf0610851429 6 10852428 1.78E-06 5.92E-07
vg0503403002 sf0503402979 5 3403002 3.38E-06 7.11E-07