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 mr1907 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
vg0524488054 sf0524425475 5 24488054 3.96E-47 4.03E-25
vg0524598692 sf0524536112 5 24598692 4.58E-47 4.45E-27
vg0524598675 sf0524536095 5 24598675 5.98E-47 4.46E-27
vg1100144812 sf1100143813 11 144812 1.91E-19 NA
vg0604087909 sf0604086910 6 4087909 3.94E-17 NA
vg0524331456 sf0524268875 5 24331456 8.63E-16 2.34E-07
vg1100109327 sf1100108327 11 109327 9.84E-15 2.28E-07
vg1200003632 sf1200002632 12 3632 4.66E-14 NA
vg0230082779 sf0230076910 2 30082779 3.86E-13 1.13E-06
vg0822365872 sf0822363159 8 22365872 2.12E-11 4.94E-07
vg1208947655 sf1208945063 12 8947655 1.16E-08 2.03E-06
vg1116101996 sf1115636868 11 16101996 1.40E-08 NA
vg0601598971 sf0601597972 6 1598971 1.82E-08 3.56E-06
vg0217028559 sf0217022689 2 17028559 NA 8.86E-08
vg0502041473 sf0502041455 5 2041473 NA 5.88E-07
vg0403670833 sf0403666439 4 3670833 NA 1.77E-06
vg0217257265 sf0217251395 2 17257265 NA 4.08E-06