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 mr1950 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
vg0405539066 sf0405534507 4 5539066 4.93E-11 2.34E-06
vg0405710877 sf0405706316 4 5710877 6.36E-11 NA
vg0406199430 sf0406194870 4 6199430 1.71E-10 NA
vg0222060419 sf0222054550 2 22060419 3.03E-10 NA
vg0715405360 sf0715404367 7 15405360 3.30E-10 NA
vg0726369741 sf0726368747 7 26369741 3.62E-10 NA
vg0715381494 sf0715380501 7 15381494 8.14E-10 1.98E-06
vg0919836933 sf0919836452 9 19836933 3.17E-07 NA
vg1004372976 sf1004389514 10 4372976 NA 3.25E-06