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 mr1183 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
vg0222739831 sf0222733962 2 22739831 6.22E-22 2.26E-19
vg0726946907 sf0726945913 7 26946907 9.59E-14 NA
vg0809343839 sf0809342843 8 9343839 8.63E-13 NA
vg0805552357 sf0805551360 8 5552357 1.83E-12 NA
vg1102216506 sf1102212364 11 2216506 7.01E-12 NA
vg1008071640 sf1007972597 10 8071640 2.28E-10 1.04E-06
vg0223811992 sf0223783239 2 23811992 3.63E-09 6.05E-08
vg1008839677 sf1008768539 10 8839677 3.93E-09 NA
vg0224382271 sf0224376402 2 24382271 5.45E-08 5.95E-08
vg0223668140 sf0223662271 2 23668140 3.67E-07 2.32E-06
vg0222683860 sf0222677991 2 22683860 NA 2.10E-06
vg0622436576 sf0622435579 6 22436576 NA 2.86E-06
vg0825887514 sf0825884800 8 25887514 NA 3.25E-06
vg0716335289 sf0716334296 7 16335289 NA 4.77E-06
vg0728664025 sf0728663033 7 28664025 NA 4.90E-06