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
vg0916776579 sf0916775578 9 16776579 5.27E-28 8.41E-16
vg1203687735 sf1203686734 12 3687735 2.11E-15 4.99E-06
vg0918502977 sf0918501976 9 18502977 1.55E-13 NA
vg0919164093 sf0919163682 9 19164093 4.63E-13 NA
vg1217086772 sf1217080727 12 17086772 5.68E-13 NA
vg0600564089 sf0600563090 6 564089 5.70E-11 NA
vg0112995841 sf0112994815 1 12995841 1.09E-10 9.38E-06
vg0918045391 sf0918044390 9 18045391 1.53E-09 3.56E-06
vg0919270981 sf0919270571 9 19270981 7.23E-09 3.89E-06
vg0333505948 sf0333498818 3 33505948 5.26E-08 7.41E-07
vg0916259556 sf0916258555 9 16259556 NA 2.91E-09
vg0107324892 sf0107323892 1 7324892 NA 9.60E-08
vg0333652898 sf0333645768 3 33652898 NA 2.59E-07
vg0607378850 sf0607377851 6 7378850 NA 2.73E-07
vg0107332683 sf0107331683 1 7332683 NA 2.96E-07
vg0522020155 sf0521957597 5 22020155 NA 7.74E-07
vg0316396424 sf0316395069 3 16396424 NA 1.25E-06
vg0408191145 sf0408186419 4 8191145 NA 1.72E-06
vg1118396844 sf1117930704 11 18396844 NA 3.04E-06
vg0617997472 sf0617996475 6 17997472 NA 3.99E-06
vg0305243308 sf0305242308 3 5243308 NA 4.20E-06
vg0816197134 sf0816194420 8 16197134 NA 4.62E-06
vg0617996660 sf0617995663 6 17996660 NA 4.66E-06
vg0917125655 sf0917124654 9 17125655 NA 4.82E-06
vg0220014490 sf0220008622 2 20014490 NA 5.00E-06