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 mr1147 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
vg1004296464 sf1004313002 10 4296464 3.62E-09 1.80E-06
vg1006943122 sf1006958745 10 6943122 4.61E-09 2.77E-06
vg1010479547 sf1010408368 10 10479547 1.40E-08 5.85E-06
vg1104978749 sf1104974560 11 4978749 1.71E-08 7.15E-06
vg0207043918 sf0207043918 2 7043918 2.04E-08 2.91E-06
vg1009415346 sf1009344167 10 9415346 5.24E-08 2.93E-08
vg1109949998 sf1109944575 11 9949998 3.59E-07 1.59E-06
vg0412457639 sf0412448354 4 12457639 5.50E-07 3.44E-07
vg0204345674 sf0204345671 2 4345674 9.07E-07 3.38E-06
vg0819603039 sf0819600326 8 19603039 1.51E-06 NA
vg1118024765 sf1117558623 11 18024765 1.65E-06 2.39E-06
vg0805469573 sf0805468576 8 5469573 NA 7.33E-06