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 mr1922 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
vg0820974361 sf0820971648 8 20974361 6.11E-27 6.77E-07
vg1219661684 sf1219633154 12 19661684 3.79E-26 4.28E-06
vg0915584040 sf0915583039 9 15584040 4.91E-25 7.25E-06
vg1207185563 sf1207182953 12 7185563 5.04E-25 5.73E-06
vg0126828419 sf0126827375 1 26828419 1.46E-24 NA
vg1219943666 sf1219915136 12 19943666 3.30E-24 1.59E-06
vg1207772422 sf1207769828 12 7772422 5.31E-23 1.36E-06
vg0127027223 sf0127026179 1 27027223 6.56E-23 4.14E-06
vg0518984986 sf0518922470 5 18984986 6.78E-21 4.74E-06
vg0712904455 sf0712903462 7 12904455 9.12E-21 NA
vg0434381347 sf0434196241 4 34381347 1.01E-20 NA
vg0432523363 sf0432338255 4 32523363 NA 4.64E-08
vg0315803692 sf0315802339 3 15803692 NA 6.36E-07
vg0323951924 sf0323950098 3 23951924 NA 1.82E-06
vg1108425600 sf1108420210 11 8425600 NA 3.39E-06