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 mr1167 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
vg0404327458 sf0404323063 4 4327458 1.59E-25 NA
vg0701559521 sf0701558521 7 1559521 3.43E-25 NA
vg0710776650 sf0710775656 7 10776650 3.61E-23 NA
vg0619653506 sf0619652509 6 19653506 5.38E-23 NA
vg0604586643 sf0604585644 6 4586643 3.69E-22 NA
vg0912448061 sf0912447060 9 12448061 2.39E-19 NA
vg0430646747 sf0430461622 4 30646747 1.08E-18 3.09E-07
vg0408658440 sf0408653716 4 8658440 NA 6.21E-07
vg0404430685 sf0404426289 4 4430685 NA 9.70E-07
vg0404403925 sf0404399529 4 4403925 NA 1.58E-06
vg0722992016 sf0722991023 7 22992016 NA 1.87E-06
vg1110034908 sf1110029485 11 10034908 NA 3.16E-06
vg0816083596 sf0816080882 8 16083596 NA 4.33E-06
vg0404456120 sf0404451724 4 4456120 NA 4.45E-06
vg0805288335 sf0805287338 8 5288335 NA 4.89E-06
vg0607359009 sf0607358010 6 7359009 NA 7.00E-06