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 mr1118 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
vg1006839627 sf1006855250 10 6839627 2.88E-33 1.15E-14
vg1006540721 sf1006556344 10 6540721 2.96E-31 9.03E-15
vg1009540574 sf1009469395 10 9540574 1.63E-25 5.23E-14
vg1009530059 sf1009458880 10 9530059 2.98E-25 2.17E-14
vg1009130355 sf1009059216 10 9130355 1.68E-24 1.32E-12
vg0407825479 sf0407820747 4 7825479 1.76E-23 9.50E-11
vg1216843191 sf1216837145 12 16843191 1.51E-22 8.72E-11
vg0142683989 sf0142682945 1 42683989 7.76E-22 3.88E-09
vg0407824609 sf0407819877 4 7824609 1.69E-21 4.63E-08
vg0403206873 sf0403202476 4 3206873 2.82E-20 2.98E-07
vg0813652209 sf0813649494 8 13652209 5.28E-20 1.50E-07
vg0403205033 sf0403200636 4 3205033 5.72E-19 3.47E-09
vg1204314449 sf1204313437 12 4314449 7.60E-19 8.97E-08
vg0714477799 sf0714476806 7 14477799 8.28E-18 2.24E-06
vg0528707749 sf0528645104 5 28707749 3.81E-17 8.89E-08
vg1002973972 sf1002972949 10 2973972 4.15E-17 2.92E-08
vg0710897803 sf0710896809 7 10897803 4.21E-17 1.35E-06
vg0110929029 sf0110928005 1 10929029 1.23E-16 1.08E-06
vg0716827828 sf0716826835 7 16827828 1.17E-15 6.62E-07
vg0525897215 sf0525834636 5 25897215 7.45E-15 2.15E-08