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 mr1193 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
vg0327430028 sf0327423081 3 27430028 2.29E-15 9.50E-10
vg0327580115 sf0327573168 3 27580115 5.40E-14 1.54E-11
vg0327523224 sf0327516277 3 27523224 1.09E-12 3.66E-09
vg0327700335 sf0327693388 3 27700335 3.22E-12 1.08E-08
vg0327696550 sf0327689603 3 27696550 2.53E-11 1.68E-07
vg0326661478 sf0326654532 3 26661478 8.24E-10 NA
vg0526439140 sf0526376503 5 26439140 2.79E-09 NA
vg1215630177 sf1215627474 12 15630177 3.35E-08 3.48E-06
vg1210753920 sf1210751284 12 10753920 2.93E-06 NA
vg0529528212 sf0529465567 5 29528212 7.85E-06 NA
vg0515641078 sf0515583619 5 15641078 NA 2.47E-06
vg0407666707 sf0407661974 4 7666707 NA 7.17E-06