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 mr1076 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
vg0719133785 sf0719132792 7 19133785 1.73E-17 2.04E-11
vg0719007567 sf0719006574 7 19007567 3.51E-16 6.18E-12
vg0719011406 sf0719010413 7 19011406 2.40E-15 5.92E-12
vg1201694296 sf1201693294 12 1694296 3.90E-14 3.90E-08
vg0719136383 sf0719135390 7 19136383 NA 2.08E-07
vg0718985954 sf0718984961 7 18985954 NA 3.03E-07
vg0704308852 sf0704307853 7 4308852 NA 4.89E-07
vg0704373499 sf0704372500 7 4373499 NA 7.80E-07
vg0624862159 sf0624861162 6 24862159 NA 9.73E-07
vg0718998483 sf0718997490 7 18998483 NA 1.01E-06
vg1009450763 sf1009379584 10 9450763 NA 1.46E-06
vg0503840950 sf0503840927 5 3840950 NA 2.20E-06
vg0719725023 sf0719724030 7 19725023 NA 2.34E-06
vg0611422032 sf0611421033 6 11422032 NA 2.52E-06
vg0707881452 sf0707880457 7 7881452 NA 3.73E-06
vg0412457639 sf0412448354 4 12457639 NA 4.56E-06