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 mr1168 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
vg0700233324 sf0700232324 7 233324 8.93E-09 4.53E-06
vg1000221182 sf1000220182 10 221182 1.48E-08 1.23E-06
vg1000080276 sf1000079276 10 80276 3.23E-08 8.54E-07
vg1018126750 sf1018055521 10 18126750 3.43E-08 5.63E-06
vg0900043410 sf0900042410 9 43410 4.53E-08 1.46E-06
vg1216681957 sf1216675911 12 16681957 8.11E-08 NA
vg0900044105 sf0900043105 9 44105 8.80E-08 1.36E-06
vg0133436043 sf0133434999 1 33436043 4.13E-07 6.75E-08
vg0906481589 sf0906480589 9 6481589 8.42E-07 3.97E-06
vg1004031418 sf1004030394 10 4031418 1.81E-06 NA