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 mr1530 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
vg1125257892 sf1124791732 11 25257892 7.93E-20 3.77E-14
vg0430573771 sf0430388646 4 30573771 1.49E-14 1.19E-08
vg0430554222 sf0430369097 4 30554222 3.41E-14 1.04E-08
vg0430549128 sf0430364003 4 30549128 7.39E-14 1.70E-08
vg1125369580 sf1124903420 11 25369580 2.90E-12 1.44E-10
vg0917084640 sf0917083639 9 17084640 1.51E-11 NA
vg0606016572 sf0606015573 6 6016572 1.24E-10 NA
vg0921847328 sf0921846847 9 21847328 1.05E-09 2.21E-07
vg0313016014 sf0313014732 3 13016014 3.48E-09 1.85E-06
vg1016277792 sf1016206568 10 16277792 1.73E-08 5.70E-09
vg0430856840 sf0430671720 4 30856840 1.76E-08 2.98E-06
vg1116397469 sf1115932346 11 16397469 7.30E-07 1.27E-06
vg0820203875 sf0820201162 8 20203875 NA 1.24E-07
vg1125263882 sf1124797722 11 25263882 NA 3.63E-07
vg1116393698 sf1115928575 11 16393698 NA 4.75E-07
vg1015834424 sf1015763194 10 15834424 NA 1.63E-06
vg1125264457 sf1124798297 11 25264457 NA 2.38E-06
vg0202261095 sf0202261095 2 2261095 NA 2.95E-06
vg0313852227 sf0313850944 3 13852227 NA 3.80E-06