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 mr1515 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
vg0527237297 sf0527174653 5 27237297 1.04E-24 NA
vg0107395608 sf0107394608 1 7395608 1.05E-24 7.99E-06
vg0702068989 sf0702067990 7 2068989 2.72E-24 NA
vg0608138693 sf0608137694 6 8138693 4.05E-24 NA
vg0802054978 sf0802053981 8 2054978 1.79E-23 7.66E-07
vg0107385646 sf0107384646 1 7385646 1.03E-21 NA
vg0327424324 sf0327417377 3 27424324 NA 9.76E-08
vg0628001136 sf0628000138 6 28001136 NA 5.53E-07
vg0327425445 sf0327418498 3 27425445 NA 7.02E-07
vg1006251648 sf1006267271 10 6251648 NA 8.09E-07
vg0400362758 sf0400361756 4 362758 NA 9.94E-07
vg0907844471 sf0907843471 9 7844471 NA 1.18E-06
vg1127981469 sf1127509855 11 27981469 NA 1.55E-06
vg1006015012 sf1006031550 10 6015012 NA 1.58E-06
vg1002941120 sf1002940097 10 2941120 NA 1.87E-06
vg1113326039 sf1112862360 11 13326039 NA 1.98E-06
vg1003223593 sf1003222570 10 3223593 NA 2.18E-06
vg0628765614 sf0628764616 6 28765614 NA 2.44E-06
vg0202726566 sf0202726564 2 2726566 NA 3.27E-06
vg1009009289 sf1008938150 10 9009289 NA 3.94E-06