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 mr1134 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
vg0138120179 sf0138119136 1 38120179 6.25E-38 7.19E-20
vg0137919286 sf0137918243 1 37919286 6.51E-38 4.95E-23
vg0812109370 sf0812108375 8 12109370 8.80E-13 NA
vg0138695323 sf0138694280 1 38695323 5.23E-11 9.90E-06
vg0208267970 sf0208267969 2 8267970 7.27E-11 NA
vg0518335953 sf0518275439 5 18335953 1.04E-10 NA
vg1112669284 sf1112205605 11 12669284 1.16E-10 1.63E-06
vg0811678191 sf0811677196 8 11678191 5.22E-09 1.10E-07
vg1007489797 sf1007505420 10 7489797 1.94E-08 9.41E-07
vg0135180752 sf0135179709 1 35180752 5.12E-08 2.18E-06
vg0331809182 sf0331802059 3 31809182 NA 1.81E-07
vg0138727130 sf0138726087 1 38727130 NA 4.40E-07
vg1117402464 sf1116936317 11 17402464 NA 9.90E-07
vg1216552747 sf1216550040 12 16552747 NA 1.92E-06
vg0910616659 sf0910615658 9 10616659 NA 2.09E-06
vg0316166709 sf0316165356 3 16166709 NA 2.74E-06
vg0112881406 sf0112880380 1 12881406 NA 2.96E-06
vg0515369335 sf0515311876 5 15369335 NA 3.38E-06