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 mr1205 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
vg0207238898 sf0207238898 2 7238898 7.60E-18 NA
vg0910748564 sf0910747563 9 10748564 1.01E-17 NA
vg1001183960 sf1001182937 10 1183960 1.47E-17 NA
vg1120726313 sf1120260216 11 20726313 1.52E-17 NA
vg0211600666 sf0211600662 2 11600666 3.97E-17 NA
vg1125628490 sf1125162329 11 25628490 2.35E-16 4.58E-08
vg0205809596 sf0205809596 2 5809596 3.51E-14 NA
vg1227320261 sf1227286661 12 27320261 6.31E-14 NA
vg0103185620 sf0103184620 1 3185620 2.69E-12 3.05E-06
vg1213935504 sf1213932842 12 13935504 NA 1.70E-06
vg1203658518 sf1203657517 12 3658518 NA 6.66E-06