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 mr1034 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
vg0113349472 sf0113348446 1 13349472 1.13E-17 8.32E-08
vg0130113615 sf0130112570 1 30113615 4.29E-17 NA
vg0626631482 sf0626630485 6 26631482 4.86E-17 NA
vg0118369451 sf0118368405 1 18369451 1.02E-16 3.63E-06
vg0402407291 sf0402402886 4 2407291 1.17E-16 NA
vg0116329592 sf0116328566 1 16329592 3.17E-16 1.67E-06
vg0905340944 sf0905339944 9 5340944 1.38E-15 2.06E-06
vg0130736010 sf0130734966 1 30736010 5.45E-15 NA
vg0410126275 sf0410116972 4 10126275 6.97E-15 3.99E-07
vg0120457787 sf0120456742 1 20457787 8.25E-14 1.69E-06
vg1009887667 sf1009816488 10 9887667 1.35E-13 NA
vg0434000706 sf0433815599 4 34000706 NA 3.97E-07
vg0112449676 sf0112448650 1 12449676 NA 2.82E-06
vg0922461985 sf0922461504 9 22461985 NA 3.37E-06
vg1217108652 sf1217102607 12 17108652 NA 4.04E-06
vg0304178129 sf0304177131 3 4178129 NA 4.42E-06
vg1211588230 sf1211585566 12 11588230 NA 5.17E-06