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 mr1709 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
vg1003464531 sf1003463508 10 3464531 6.17E-127 4.25E-75
vg1003045443 sf1003044420 10 3045443 1.22E-108 2.83E-94
vg1003101362 sf1003100339 10 3101362 1.27E-76 1.55E-26
vg1003401168 sf1003400145 10 3401168 8.25E-73 4.13E-74
vg1003087335 sf1003086312 10 3087335 1.11E-65 3.95E-55
vg1003470179 sf1003469156 10 3470179 1.01E-53 7.42E-27
vg1003128189 sf1003127166 10 3128189 2.66E-46 4.11E-44
vg0717726119 sf0717725126 7 17726119 2.02E-37 3.46E-12
vg1003093102 sf1003092079 10 3093102 1.05E-36 2.15E-26
vg0710493875 sf0710492881 7 10493875 1.69E-36 4.93E-09
vg0717726887 sf0717725894 7 17726887 2.12E-34 4.36E-15
vg0403728354 sf0403723960 4 3728354 3.10E-31 6.93E-13
vg1209942785 sf1209940195 12 9942785 5.75E-30 1.19E-11
vg0909393050 sf0909392049 9 9393050 8.75E-29 1.63E-13
vg0909083757 sf0909082756 9 9083757 2.95E-26 1.35E-10
vg1003523062 sf1003522039 10 3523062 3.64E-25 1.70E-23
vg0710493467 sf0710492473 7 10493467 3.94E-25 5.41E-10
vg0422509978 sf0422324865 4 22509978 1.65E-23 2.79E-14
vg1003599620 sf1003598597 10 3599620 1.20E-21 7.16E-15
vg1002154039 sf1002153016 10 2154039 5.73E-20 3.06E-12
vg1003340833 sf1003339810 10 3340833 1.75E-15 1.59E-20
vg0623386254 sf0623385257 6 23386254 9.24E-12 5.43E-14
vg1003688387 sf1003687364 10 3688387 4.81E-10 1.31E-09
vg1003467337 sf1003466314 10 3467337 1.86E-09 5.48E-08
vg1003053735 sf1003052712 10 3053735 5.85E-09 1.70E-13
vg1003461178 sf1003460155 10 3461178 NA 8.27E-15
vg0608717175 sf0608716176 6 8717175 NA 2.57E-09