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 mr1329 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
vg0607991416 sf0607990417 6 7991416 5.45E-10 5.71E-07
vg0421031215 sf0420859268 4 21031215 1.05E-09 7.81E-08
vg0421028122 sf0420856175 4 21028122 1.22E-09 6.46E-08
vg0424926413 sf0424741274 4 24926413 3.91E-09 3.26E-06
vg0922183366 sf0922182885 9 22183366 2.23E-08 NA
vg0717084736 sf0717083743 7 17084736 2.84E-08 NA
vg0907175535 sf0907174535 9 7175535 3.14E-08 4.25E-06
vg0521659473 sf0521596915 5 21659473 1.17E-07 9.15E-07
vg0232755756 sf0232749887 2 32755756 1.28E-07 1.92E-06
vg0704864945 sf0704863946 7 4864945 1.33E-06 9.12E-08
vg0223525077 sf0223519208 2 23525077 1.77E-06 4.13E-06
vg0420718113 sf0420546156 4 20718113 3.45E-06 5.13E-08
vg0416747657 sf0416575701 4 16747657 5.63E-06 1.44E-06
vg0516508609 sf0516451091 5 16508609 7.90E-06 3.01E-07
vg0607659813 sf0607658814 6 7659813 NA 9.40E-07
vg0403204105 sf0403199708 4 3204105 NA 2.61E-06
vg0421384856 sf0421212909 4 21384856 NA 2.88E-06
vg1224447613 sf1224414066 12 24447613 NA 3.71E-06