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 mr1149 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
vg0421352076 sf0421180130 4 21352076 3.90E-09 NA
vg0402093212 sf0402088806 4 2093212 1.20E-08 NA
vg0810864582 sf0810863587 8 10864582 1.92E-08 NA
vg0725422656 sf0725421662 7 25422656 3.92E-08 NA
vg1207672832 sf1207670236 12 7672832 9.20E-08 NA
vg1015507336 sf1015436104 10 15507336 4.88E-07 NA
vg0400675893 sf0400674892 4 675893 1.49E-06 3.87E-06
vg0905076333 sf0905075333 9 5076333 7.38E-06 NA