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 mr1588 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
vg1001438303 sf1001437280 10 1438303 2.94E-35 2.24E-19
vg0529552096 sf0529489451 5 29552096 6.34E-33 3.29E-07
vg0402546694 sf0402542297 4 2546694 1.18E-31 3.29E-06
vg0804719105 sf0804718108 8 4719105 1.99E-31 2.92E-06
vg0806591666 sf0806590671 8 6591666 6.70E-30 2.37E-06
vg0807623757 sf0807622762 8 7623757 7.63E-30 3.41E-06
vg1001229577 sf1001228554 10 1229577 3.78E-29 3.42E-08
vg1001208884 sf1001207861 10 1208884 NA 7.98E-16
vg1001457313 sf1001456290 10 1457313 NA 5.92E-13
vg1001440523 sf1001439500 10 1440523 NA 2.49E-10
vg1002108639 sf1002107616 10 2108639 NA 1.11E-08
vg1002107770 sf1002106747 10 2107770 NA 2.46E-08
vg1001467114 sf1001466091 10 1467114 NA 2.56E-08
vg0806089259 sf0806088264 8 6089259 NA 3.05E-08
vg0818608910 sf0818606197 8 18608910 NA 1.06E-07
vg0804361681 sf0804360684 8 4361681 NA 1.20E-07
vg0324205406 sf0324203485 3 24205406 NA 2.17E-07
vg1219934151 sf1219905621 12 19934151 NA 2.66E-07
vg1219908853 sf1219880323 12 19908853 NA 3.13E-07
vg0806118132 sf0806117137 8 6118132 NA 4.46E-07
vg0807428848 sf0807427853 8 7428848 NA 4.60E-07
vg0322577513 sf0322576002 3 22577513 NA 8.38E-07
vg0807724740 sf0807723745 8 7724740 NA 9.37E-07
vg0503469093 sf0503469070 5 3469093 NA 1.01E-06
vg0102595003 sf0102594003 1 2595003 NA 1.17E-06
vg0412555488 sf0412546198 4 12555488 NA 1.41E-06
vg0804590579 sf0804589582 8 4590579 NA 1.66E-06
vg0403668263 sf0403663869 4 3668263 NA 1.96E-06
vg1226907992 sf1226874391 12 26907992 NA 2.06E-06
vg1002248885 sf1002247862 10 2248885 NA 2.44E-06