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 mr1441 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
vg0222742146 sf0222736277 2 22742146 2.09E-84 4.89E-35
vg0222719698 sf0222713829 2 22719698 7.50E-84 4.64E-36
vg0601859864 sf0601858865 6 1859864 2.32E-33 NA
vg0701995362 sf0701994363 7 1995362 4.59E-33 NA
vg1017965135 sf1017893907 10 17965135 6.90E-33 NA
vg0705549134 sf0705548135 7 5549134 9.80E-33 NA
vg0600808677 sf0600807678 6 808677 7.22E-30 NA
vg0816278155 sf0816275441 8 16278155 1.40E-27 4.90E-06
vg0600305239 sf0600304239 6 305239 5.55E-27 NA
vg0222725003 sf0222719134 2 22725003 NA 5.95E-16
vg0223769163 sf0223763294 2 23769163 NA 1.75E-07
vg0224382271 sf0224376402 2 24382271 NA 6.13E-07
vg0332475968 sf0332468841 3 32475968 NA 7.80E-07
vg0222807259 sf0222801390 2 22807259 NA 1.14E-06
vg0224259730 sf0224253861 2 24259730 NA 4.42E-06