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 mr1552 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
vg0608756076 sf0608755077 6 8756076 1.26E-23 NA
vg0915361320 sf0915360319 9 15361320 1.94E-19 NA
vg0126148298 sf0126147254 1 26148298 2.77E-19 NA
vg0715669213 sf0715668220 7 15669213 3.04E-19 NA
vg0220361684 sf0220355816 2 20361684 6.79E-19 NA
vg0608080579 sf0608079580 6 8080579 2.02E-17 1.67E-06
vg1011061499 sf1010990319 10 11061499 7.71E-16 4.46E-06
vg0607501602 sf0607500603 6 7501602 2.78E-15 NA
vg0220806171 sf0220800303 2 20806171 5.08E-14 NA
vg0218664196 sf0218658327 2 18664196 NA 1.55E-06
vg0400676505 sf0400675504 4 676505 NA 7.96E-06