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 mr1026 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
vg1008776633 sf1008705495 10 8776633 3.55E-28 4.04E-12
vg1007456082 sf1007471705 10 7456082 3.44E-27 1.20E-14
vg0403206873 sf0403202476 4 3206873 6.63E-24 2.21E-09
vg0407824609 sf0407819877 4 7824609 1.51E-23 3.21E-07
vg0528707739 sf0528645094 5 28707739 5.32E-23 1.07E-08
vg1006028591 sf1006045129 10 6028591 6.35E-22 7.90E-10
vg0142683989 sf0142682945 1 42683989 2.25E-21 1.02E-07
vg1006533973 sf1006549596 10 6533973 7.90E-21 6.83E-11
vg1009530878 sf1009459699 10 9530878 2.44E-19 7.32E-10
vg1010146858 sf1010075679 10 10146858 3.33E-19 1.33E-06
vg0110929029 sf0110928005 1 10929029 8.32E-18 7.19E-07
vg1216843191 sf1216837145 12 16843191 4.44E-13 3.96E-06
vg0317087788 sf0317086602 3 17087788 NA 2.15E-07
vg1005555783 sf1005572320 10 5555783 NA 1.34E-06
vg1009935788 sf1009864609 10 9935788 NA 2.15E-06
vg1004963409 sf1004979946 10 4963409 NA 4.02E-06