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 mr1645 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
vg1223875210 sf1223841663 12 23875210 1.87E-12 1.58E-06
vg1209263213 sf1209260622 12 9263213 9.54E-11 NA
vg1209257213 sf1209254622 12 9257213 1.27E-10 NA
vg0317235751 sf0317234561 3 17235751 1.47E-10 NA
vg0907939520 sf0907938520 9 7939520 1.69E-10 NA
vg0507336970 sf0507336912 5 7336970 2.69E-10 NA
vg1010927325 sf1010856145 10 10927325 6.66E-10 1.38E-06
vg1010726638 sf1010655459 10 10726638 4.63E-09 4.17E-06
vg0516841556 sf0516781197 5 16841556 6.24E-09 2.16E-06
vg0701188868 sf0701187868 7 1188868 2.02E-08 3.17E-06
vg0718397736 sf0718396743 7 18397736 NA 3.72E-07
vg0726559137 sf0726558143 7 26559137 NA 1.80E-06
vg0819105437 sf0819102724 8 19105437 NA 1.95E-06
vg1010751750 sf1010680571 10 10751750 NA 3.13E-06