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 mr1524 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
vg0421028117 sf0420856170 4 21028117 1.85E-09 1.95E-07
vg0421020772 sf0420848825 4 21020772 1.94E-09 1.73E-07
vg0607991416 sf0607990417 6 7991416 2.14E-09 1.75E-06
vg0127776647 sf0127775603 1 27776647 3.17E-09 5.21E-06
vg0424926413 sf0424741274 4 24926413 4.38E-09 3.94E-06
vg1020529341 sf1020457820 10 20529341 5.83E-09 2.52E-06
vg1106552685 sf1106548438 11 6552685 1.29E-08 2.41E-06
vg0232755756 sf0232749887 2 32755756 1.94E-08 3.23E-07
vg0721470198 sf0721469205 7 21470198 2.69E-08 NA
vg0817853841 sf0817851128 8 17853841 1.81E-07 4.17E-06
vg0223525077 sf0223519208 2 23525077 2.35E-07 4.03E-07
vg0416747657 sf0416575701 4 16747657 1.64E-06 5.69E-07
vg0516508609 sf0516451091 5 16508609 7.00E-06 1.45E-07
vg0704864945 sf0704863946 7 4864945 9.33E-06 6.62E-07
vg0420718113 sf0420546156 4 20718113 NA 1.78E-07
vg1215307750 sf1215305048 12 15307750 NA 9.06E-07
vg0607659813 sf0607658814 6 7659813 NA 1.80E-06
vg0817557507 sf0817554793 8 17557507 NA 1.88E-06
vg1224447613 sf1224414066 12 24447613 NA 2.16E-06
vg0404029438 sf0404025045 4 4029438 NA 4.20E-06