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 mr1914 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
vg0217124073 sf0217118203 2 17124073 1.23E-20 2.44E-15
vg1216728542 sf1216722496 12 16728542 3.33E-10 2.53E-07
vg0217285572 sf0217279702 2 17285572 7.42E-09 1.17E-06
vg1005364284 sf1005380821 10 5364284 1.79E-08 NA
vg0907127691 sf0907126691 9 7127691 3.96E-08 NA
vg0216335484 sf0216329614 2 16335484 3.60E-07 1.02E-06
vg1004194444 sf1004143764 10 4194444 9.47E-07 NA
vg1122377284 sf1121911155 11 22377284 6.26E-06 1.82E-06