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 mr1929 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
vg0222725003 sf0222719134 2 22725003 5.97E-33 6.31E-18
vg0222567385 sf0222561516 2 22567385 1.02E-27 4.50E-18
vg0222725103 sf0222719234 2 22725103 8.63E-24 1.04E-38
vg0222740991 sf0222735122 2 22740991 5.01E-23 1.29E-39
vg0222729853 sf0222723984 2 22729853 9.28E-18 3.25E-11
vg0224533056 sf0224527187 2 24533056 1.23E-14 1.40E-09
vg0139785874 sf0139784831 1 39785874 4.38E-14 NA
vg0221929594 sf0221923725 2 21929594 7.08E-14 1.81E-07
vg0224678499 sf0224672630 2 24678499 1.12E-13 7.90E-08
vg0222729132 sf0222723263 2 22729132 3.70E-12 2.43E-07
vg0204342935 sf0204342932 2 4342935 3.09E-11 NA
vg0208709176 sf0208709175 2 8709176 5.71E-10 2.40E-06
vg0220530033 sf0220524165 2 20530033 9.55E-10 4.14E-06
vg0208783416 sf0208783414 2 8783416 2.90E-09 4.79E-06
vg0223668413 sf0223662544 2 23668413 NA 1.05E-06
vg0221650044 sf0221644175 2 21650044 NA 1.17E-06
vg0223736835 sf0223730966 2 23736835 NA 1.26E-06
vg0222703153 sf0222697284 2 22703153 NA 1.33E-06
vg0224820181 sf0224814312 2 24820181 NA 1.40E-06
vg0208783825 sf0208783823 2 8783825 NA 2.19E-06
vg0208856189 sf0208856187 2 8856189 NA 2.66E-06
vg0208855384 sf0208855382 2 8855384 NA 3.26E-06
vg1112606022 sf1112142225 11 12606022 NA 3.31E-06
vg0222801968 sf0222796099 2 22801968 NA 3.81E-06