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 mr1834 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
vg0609394618 sf0609393619 6 9394618 2.48E-10 NA
vg0333760698 sf0333753568 3 33760698 2.95E-10 NA
vg0725111360 sf0725110366 7 25111360 1.07E-09 NA
vg0909128170 sf0909127169 9 9128170 2.82E-09 NA
vg1022149399 sf1022077873 10 22149399 3.50E-09 NA
vg0718004907 sf0718003914 7 18004907 5.80E-09 2.18E-06
vg1010257353 sf1010186174 10 10257353 6.55E-08 NA
vg0433122732 sf0432937621 4 33122732 1.35E-07 4.86E-06
vg1227463510 sf1227429910 12 27463510 1.41E-07 NA
vg0333662864 sf0333655734 3 33662864 7.47E-07 6.28E-07
vg0508125097 sf0508125037 5 8125097 NA 2.06E-06
vg1109940557 sf1109935134 11 9940557 NA 8.77E-06