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 mr1085 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 5.80E-16 7.49E-11
vg0719007567 sf0719006574 7 19007567 7.39E-15 2.46E-11
vg1201735910 sf1201734908 12 1735910 1.69E-13 8.85E-09
vg1201736330 sf1201735328 12 1736330 1.98E-13 6.54E-09
vg0719136412 sf0719135419 7 19136412 4.15E-12 4.78E-09
vg0707583684 sf0707582689 7 7583684 3.84E-11 4.48E-07
vg0315179733 sf0315178380 3 15179733 4.34E-11 4.94E-06
vg0315178899 sf0315177546 3 15178899 8.25E-11 7.94E-07
vg0718985745 sf0718984752 7 18985745 NA 5.09E-07
vg0503840950 sf0503840927 5 3840950 NA 5.70E-07
vg0719725023 sf0719724030 7 19725023 NA 1.16E-06
vg1201451787 sf1201450787 12 1451787 NA 1.34E-06
vg0718998483 sf0718997490 7 18998483 NA 1.42E-06
vg0805469573 sf0805468576 8 5469573 NA 2.41E-06
vg0704373499 sf0704372500 7 4373499 NA 2.47E-06
vg1201385569 sf1201384569 12 1385569 NA 2.49E-06
vg1201512648 sf1201511648 12 1512648 NA 3.36E-06
vg0305031973 sf0305030975 3 5031973 NA 4.92E-06
vg1106375766 sf1106371518 11 6375766 NA 8.06E-06