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 mr1317 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
vg0217095683 sf0217089813 2 17095683 1.77E-52 2.28E-29
vg0217085164 sf0217079294 2 17085164 1.05E-33 4.53E-22
vg0217940314 sf0217934445 2 17940314 1.70E-22 6.57E-12
vg1015182572 sf1015111340 10 15182572 1.16E-21 1.88E-06
vg1015182556 sf1015111324 10 15182556 1.29E-21 1.68E-06
vg1220336354 sf1220307796 12 20336354 1.78E-21 2.12E-07
vg1108225523 sf1108220133 11 8225523 5.90E-20 5.81E-08
vg0217233564 sf0217227694 2 17233564 2.72E-14 7.35E-07
vg0218543938 sf0218538069 2 18543938 1.98E-11 1.42E-09
vg0217474288 sf0217468418 2 17474288 2.15E-11 8.85E-08
vg0212591710 sf0212591706 2 12591710 6.37E-11 6.91E-08
vg0217524100 sf0217518230 2 17524100 3.28E-10 5.45E-09
vg0216239744 sf0216233874 2 16239744 3.42E-10 4.01E-06
vg0217125730 sf0217119860 2 17125730 NA 1.29E-10
vg0217497082 sf0217491212 2 17497082 NA 1.55E-10
vg0217025287 sf0217019417 2 17025287 NA 4.66E-10
vg0217221174 sf0217215304 2 17221174 NA 1.25E-07
vg0217027791 sf0217021921 2 17027791 NA 4.73E-07
vg0208695804 sf0208695803 2 8695804 NA 1.08E-06
vg0215745955 sf0215740085 2 15745955 NA 1.57E-06
vg0210811556 sf0210811554 2 10811556 NA 2.24E-06
vg0218489541 sf0218483672 2 18489541 NA 3.63E-06