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 mr1013 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
vg1208149893 sf1208147299 12 8149893 8.41E-20 NA
vg0125768624 sf0125767580 1 25768624 2.93E-18 1.76E-06
vg0130113615 sf0130112570 1 30113615 4.41E-18 NA
vg0605415117 sf0605414118 6 5415117 4.80E-18 NA
vg0517981962 sf0517921448 5 17981962 6.52E-18 NA
vg1009167831 sf1009096652 10 9167831 4.64E-16 2.85E-06
vg0526967577 sf0526904933 5 26967577 1.02E-14 6.85E-07
vg0434000706 sf0433815599 4 34000706 1.71E-14 1.35E-09
vg1209271838 sf1209269248 12 9271838 3.82E-14 7.73E-09
vg0522130001 sf0522067443 5 22130001 8.69E-14 3.91E-06
vg0226051634 sf0226045765 2 26051634 3.90E-13 2.74E-06
vg1020829960 sf1020758439 10 20829960 NA 2.28E-07
vg0905473217 sf0905472217 9 5473217 NA 3.90E-07
vg1020360604 sf1020289084 10 20360604 NA 6.56E-07
vg0906112024 sf0906111024 9 6112024 NA 8.98E-07
vg1202574324 sf1202573326 12 2574324 NA 1.84E-06
vg0525142447 sf0525079868 5 25142447 NA 1.86E-06
vg0100409422 sf0100408422 1 409422 NA 3.27E-06
vg0128573807 sf0128572762 1 28573807 NA 4.59E-06
vg1209397024 sf1209394433 12 9397024 NA 7.26E-06