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 mr1863 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
vg0222743428 sf0222737559 2 22743428 3.73E-15 1.95E-13
vg0222723138 sf0222717269 2 22723138 6.62E-15 3.79E-14
vg0216971299 sf0216965429 2 16971299 2.10E-09 2.20E-07
vg0722485787 sf0722484794 7 22485787 2.42E-08 NA
vg0610865756 sf0610864757 6 10865756 2.50E-08 4.31E-06
vg0222652351 sf0222646482 2 22652351 9.57E-08 NA
vg0222725003 sf0222719134 2 22725003 9.77E-08 1.50E-07
vg1214822308 sf1214819649 12 14822308 3.82E-07 5.97E-07
vg0115899007 sf0115897981 1 15899007 NA 2.23E-06