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
vg0610146260 sf0610145261 6 10146260 3.15E-12 4.12E-08
vg0319112030 sf0319110790 3 19112030 1.01E-09 NA
vg0103143509 sf0103142509 1 3143509 1.04E-08 4.61E-07
vg0500284833 sf0500284833 5 284833 2.87E-08 NA
vg0141857437 sf0141856394 1 41857437 3.25E-08 NA
vg0610114266 sf0610113267 6 10114266 2.25E-06 7.19E-07
vg0231620755 sf0231614886 2 31620755 4.28E-06 NA
vg0723095855 sf0723094862 7 23095855 6.15E-06 NA
vg0726257978 sf0726256984 7 26257978 NA 1.84E-06
vg0715227955 sf0715226962 7 15227955 NA 2.04E-06
vg0621629913 sf0621628916 6 21629913 NA 4.03E-06