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 mr1091 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
vg0610559165 sf0610558166 6 10559165 3.29E-69 6.06E-41
vg0610566237 sf0610565238 6 10566237 3.31E-59 2.85E-42
vg0610323400 sf0610322401 6 10323400 1.88E-50 2.82E-29
vg0610776489 sf0610775490 6 10776489 3.27E-32 8.88E-20
vg0610412338 sf0610411339 6 10412338 3.77E-32 1.33E-21
vg0617223679 sf0617222682 6 17223679 4.99E-28 2.77E-06
vg0610556004 sf0610555005 6 10556004 3.19E-27 2.99E-16
vg0609894687 sf0609893688 6 9894687 1.04E-25 3.52E-15
vg0616988304 sf0616987307 6 16988304 7.10E-25 1.12E-07
vg0613442719 sf0613441720 6 13442719 9.87E-25 5.47E-07
vg0610683293 sf0610682294 6 10683293 1.34E-23 5.19E-19
vg0611574660 sf0611573661 6 11574660 5.80E-20 9.94E-13
vg0611969595 sf0611968596 6 11969595 9.75E-19 4.18E-09
vg0611493106 sf0611492107 6 11493106 2.03E-17 1.48E-10
vg0610676484 sf0610675485 6 10676484 1.98E-16 1.02E-17
vg0610447618 sf0610446619 6 10447618 8.79E-15 1.28E-12
vg0206168898 sf0206168898 2 6168898 1.18E-12 4.27E-08
vg0610442142 sf0610441143 6 10442142 1.33E-12 5.16E-13
vg0611470898 sf0611469899 6 11470898 2.24E-12 1.01E-07
vg0612043733 sf0612042734 6 12043733 2.91E-12 4.42E-10
vg0610108790 sf0610107791 6 10108790 3.28E-12 9.27E-10
vg0610752419 sf0610751420 6 10752419 4.61E-12 1.60E-09
vg0610127588 sf0610126589 6 10127588 NA 1.64E-11
vg0610211069 sf0610210070 6 10211069 NA 1.96E-08
vg0618988041 sf0618987044 6 18988041 NA 4.18E-08
vg0615150907 sf0615149908 6 15150907 NA 3.27E-07
vg0716085277 sf0716084284 7 16085277 NA 1.14E-06