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 mr1982 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
vg0421026126 sf0420854179 4 21026126 1.38E-09 8.97E-08
vg0608111689 sf0608110690 6 8111689 4.66E-09 5.20E-07
vg0907175535 sf0907174535 9 7175535 4.76E-09 4.55E-07
vg0317321849 sf0317320659 3 17321849 1.61E-08 1.17E-06
vg1106552685 sf1106548438 11 6552685 1.65E-08 2.09E-06
vg1106552386 sf1106548139 11 6552386 2.37E-08 1.70E-06
vg0525973696 sf0525911116 5 25973696 3.20E-08 4.55E-06
vg0232755756 sf0232749887 2 32755756 7.05E-08 1.31E-06
vg1206398865 sf1206397755 12 6398865 7.90E-08 4.08E-06
vg1206396445 sf1206395335 12 6396445 7.94E-08 5.82E-06
vg0521659473 sf0521596915 5 21659473 1.20E-07 3.86E-06
vg0605513869 sf0605512870 6 5513869 4.81E-07 NA
vg0808428148 sf0808427152 8 8428148 8.00E-07 9.67E-07
vg0420718113 sf0420546156 4 20718113 NA 1.49E-06
vg0516381476 sf0516323958 5 16381476 NA 4.17E-06
vg0232208358 sf0232202489 2 32208358 NA 4.43E-06