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 mr1094 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
vg0610566343 sf0610565344 6 10566343 1.30E-90 5.31E-35
vg0719209059 sf0719208066 7 19209059 1.97E-50 4.02E-07
vg0719044633 sf0719043640 7 19044633 1.34E-47 2.77E-06
vg0402287234 sf0402282829 4 2287234 1.13E-45 NA
vg0613895431 sf0613894432 6 13895431 7.73E-44 7.57E-07
vg0233932146 sf0233926277 2 33932146 7.90E-44 NA
vg0614169262 sf0614168263 6 14169262 3.73E-39 9.36E-08
vg0616988304 sf0616987307 6 16988304 5.81E-39 9.95E-10
vg0619621981 sf0619620984 6 19621981 3.62E-36 3.15E-06
vg0610763769 sf0610762770 6 10763769 NA 4.28E-13
vg0610757638 sf0610756639 6 10757638 NA 3.87E-12
vg0222727946 sf0222722077 2 22727946 NA 3.41E-11
vg0222741535 sf0222735666 2 22741535 NA 7.38E-11
vg0610102601 sf0610101602 6 10102601 NA 1.06E-09
vg0609930953 sf0609929954 6 9930953 NA 1.26E-08
vg0610014317 sf0610013318 6 10014317 NA 1.86E-08
vg0222817939 sf0222812070 2 22817939 NA 6.36E-08
vg0610444069 sf0610443070 6 10444069 NA 8.39E-08
vg0610149149 sf0610148150 6 10149149 NA 9.18E-08
vg0610813890 sf0610812891 6 10813890 NA 1.38E-07
vg0222628680 sf0222622811 2 22628680 NA 2.42E-07
vg0611845202 sf0611856608 6 11845202 NA 3.68E-07
vg0610058276 sf0610057277 6 10058276 NA 1.62E-06
vg0615282894 sf0615281895 6 15282894 NA 1.90E-06
vg0122725848 sf0122724804 1 22725848 NA 2.40E-06
vg0611882368 sf0611881369 6 11882368 NA 3.66E-06
vg0617826668 sf0617825671 6 17826668 NA 3.69E-06
vg0609903615 sf0609902616 6 9903615 NA 3.91E-06
vg0616628202 sf0616627204 6 16628202 NA 5.68E-06
vg0614574227 sf0614573228 6 14574227 NA 5.87E-06