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 mr1375 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
vg0137837925 sf0137836882 1 37837925 2.48E-36 1.40E-09
vg0137855094 sf0137854051 1 37855094 6.25E-34 8.08E-11
vg1119446198 sf1118979886 11 19446198 5.09E-30 1.49E-07
vg0134494318 sf0134493275 1 34494318 3.24E-29 NA
vg0137832701 sf0137831658 1 37832701 1.85E-28 6.47E-11
vg0104046006 sf0104045006 1 4046006 2.36E-28 NA
vg0819260437 sf0819257724 8 19260437 4.00E-27 NA
vg0134507631 sf0134506588 1 34507631 NA 1.01E-06
vg0424368741 sf0424183602 4 24368741 NA 1.22E-06
vg1209591941 sf1209589350 12 9591941 NA 2.03E-06
vg0105135512 sf0105134512 1 5135512 NA 4.55E-06
vg1209900468 sf1209897878 12 9900468 NA 9.50E-06