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 mr1543 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
vg0113615431 sf0113614405 1 13615431 1.07E-11 9.71E-09
vg0221812870 sf0221807001 2 21812870 4.51E-11 6.33E-07
vg0728682231 sf0728681239 7 28682231 1.08E-10 9.50E-07
vg1115275633 sf1114811947 11 15275633 2.98E-10 NA
vg1103485731 sf1103481634 11 3485731 1.33E-09 NA
vg0124891937 sf0124890893 1 24891937 2.00E-09 NA
vg0804877336 sf0804876339 8 4877336 1.35E-07 1.31E-06
vg1105927401 sf1105923153 11 5927401 6.33E-07 3.05E-06
vg0323005237 sf0323003725 3 23005237 NA 3.54E-07
vg1121993729 sf1121527600 11 21993729 NA 4.22E-06