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 mr1221 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
vg0610584120 sf0610583121 6 10584120 9.03E-52 1.91E-18
vg0610587398 sf0610586399 6 10587398 9.82E-51 1.48E-19
vg0610645680 sf0610644681 6 10645680 1.74E-44 3.62E-15
vg1201579161 sf1201578161 12 1579161 6.02E-35 NA
vg1010178899 sf1010107720 10 10178899 2.23E-34 NA
vg0620382387 sf0620381390 6 20382387 2.97E-34 NA
vg0616950705 sf0616949708 6 16950705 7.69E-34 NA
vg0617303575 sf0617302578 6 17303575 2.37E-31 3.89E-06
vg0629122924 sf0629121926 6 29122924 4.28E-31 1.21E-06
vg0719369847 sf0719368854 7 19369847 4.99E-28 NA
vg0610114266 sf0610113267 6 10114266 NA 4.08E-08
vg0610787522 sf0610786523 6 10787522 NA 1.67E-07
vg0610772519 sf0610771520 6 10772519 NA 2.02E-07
vg0610788671 sf0610787672 6 10788671 NA 2.94E-07
vg1111292651 sf1111286968 11 11292651 NA 7.77E-07
vg0610681498 sf0610680499 6 10681498 NA 1.30E-06
vg0719454316 sf0719453323 7 19454316 NA 1.72E-06
vg1200182981 sf1200181981 12 182981 NA 1.84E-06
vg0611903939 sf0611902940 6 11903939 NA 4.76E-06