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 mr1009 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
vg0118347734 sf0118346688 1 18347734 1.00E-09 1.00E-09
vg0901044144 sf0901043144 9 1044144 1.02E-09 1.02E-09
vg0901048761 sf0901047761 9 1048761 1.79E-09 1.79E-09
vg0203460456 sf0203460454 2 3460456 1.47E-08 1.47E-08
vg0916734760 sf0916733759 9 16734760 3.00E-08 3.00E-08
vg1220059260 sf1220030702 12 20059260 5.50E-08 5.50E-08
vg1015662665 sf1015591435 10 15662665 1.27E-07 1.27E-07
vg0904356037 sf0904355037 9 4356037 1.33E-07 1.33E-07
vg0406224825 sf0406220265 4 6224825 1.95E-07 1.95E-07
vg0124089174 sf0124088130 1 24089174 2.68E-07 2.68E-07
vg1003360615 sf1003359592 10 3360615 2.92E-07 2.92E-07
vg0729188367 sf0729187375 7 29188367 3.95E-07 3.95E-07
vg0112302656 sf0112301630 1 12302656 5.60E-07 5.60E-07
vg0130874710 sf0130873666 1 30874710 9.49E-07 9.49E-07
vg0124465629 sf0124464585 1 24465629 1.43E-06 1.43E-06
vg1219821279 sf1219792749 12 19821279 1.55E-06 1.55E-06
vg0807716778 sf0807715783 8 7716778 1.59E-06 1.59E-06
vg0905280002 sf0905279002 9 5280002 1.60E-06 1.60E-06
vg0138579441 sf0138578398 1 38579441 1.73E-06 1.73E-06
vg0630243903 sf0630242905 6 30243903 2.15E-06 2.15E-06
vg0200657074 sf0200657074 2 657074 2.54E-06 2.54E-06