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 mr1707 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
vg0918158744 sf0918157743 9 18158744 1.63E-19 1.58E-10
vg0916776579 sf0916775578 9 16776579 1.77E-18 4.67E-12
vg0916062859 sf0916061858 9 16062859 6.95E-13 6.91E-06
vg1203687735 sf1203686734 12 3687735 2.80E-09 NA
vg0919013922 sf0919012922 9 19013922 3.03E-09 NA
vg0704600543 sf0704599544 7 4600543 8.66E-09 1.25E-06
vg0107324892 sf0107323892 1 7324892 1.75E-07 2.10E-06
vg0821379569 sf0821376856 8 21379569 4.34E-07 NA
vg0107324822 sf0107323822 1 7324822 7.70E-07 3.19E-06
vg0607378048 sf0607377049 6 7378048 1.46E-06 1.04E-06
vg1115833983 sf1115370291 11 15833983 1.54E-06 1.16E-06
vg0611577534 sf0611576535 6 11577534 2.88E-06 3.50E-06
vg0816197134 sf0816194420 8 16197134 NA 3.29E-06
vg0316396424 sf0316395069 3 16396424 NA 4.56E-06