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 mr1974 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
vg0142695483 sf0142694439 1 42695483 2.22E-20 1.13E-13
vg0142632661 sf0142631617 1 42632661 2.32E-20 1.26E-13
vg0142463852 sf0142462808 1 42463852 3.55E-12 2.88E-09
vg0142373131 sf0142372087 1 42373131 4.35E-11 4.92E-06
vg0142638768 sf0142637724 1 42638768 7.42E-11 2.31E-10
vg0104472484 sf0104471484 1 4472484 1.28E-10 NA
vg0721832137 sf0721831144 7 21832137 5.95E-10 NA
vg0142686538 sf0142685494 1 42686538 9.87E-10 1.09E-10
vg0143242911 sf0143241867 1 43242911 1.60E-07 1.63E-07
vg0142706301 sf0142705257 1 42706301 8.28E-07 4.38E-06
vg0407630134 sf0407625401 4 7630134 3.49E-06 5.89E-08
vg1207844031 sf1207841437 12 7844031 9.97E-06 4.49E-06
vg1203872985 sf1203871984 12 3872985 NA 4.83E-06