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 mr1484 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
vg1125118463 sf1124652303 11 25118463 7.52E-70 1.28E-50
vg1125079736 sf1124613576 11 25079736 1.26E-33 2.71E-29
vg1125432444 sf1124966283 11 25432444 3.37E-31 2.27E-13
vg1124959930 sf1124493770 11 24959930 2.59E-30 3.18E-11
vg0105168999 sf0105167999 1 5168999 3.02E-30 2.00E-07
vg0815646521 sf0815643807 8 15646521 8.96E-30 6.39E-07
vg1124875808 sf1124409648 11 24875808 7.46E-29 2.95E-17
vg1125390548 sf1124924387 11 25390548 2.38E-26 1.05E-15
vg1124989458 sf1124523298 11 24989458 7.53E-26 4.85E-23
vg0608086564 sf0608085565 6 8086564 2.65E-25 8.02E-10
vg1124966740 sf1124500580 11 24966740 3.79E-25 2.49E-22
vg1124989620 sf1124523460 11 24989620 NA 2.61E-18
vg1125080303 sf1124614143 11 25080303 NA 1.21E-15
vg0328637867 sf0328630920 3 28637867 NA 6.82E-15
vg1125105498 sf1124639338 11 25105498 NA 1.65E-14
vg1125089512 sf1124623352 11 25089512 NA 3.95E-14
vg1124988847 sf1124522687 11 24988847 NA 5.53E-13
vg1125441578 sf1124975417 11 25441578 NA 7.40E-13
vg1124453926 sf1123987766 11 24453926 NA 1.28E-12
vg0901346489 sf0901345489 9 1346489 NA 1.04E-11
vg1125257504 sf1124791344 11 25257504 NA 6.12E-11
vg0307571121 sf0307570059 3 7571121 NA 7.39E-11
vg1124320687 sf1123854557 11 24320687 NA 2.23E-10
vg0621172424 sf0621171427 6 21172424 NA 6.53E-10
vg1122495069 sf1122028940 11 22495069 NA 9.64E-10
vg1125079769 sf1124613609 11 25079769 NA 2.15E-09
vg1125028775 sf1124562615 11 25028775 NA 3.46E-09
vg1125600946 sf1125134785 11 25600946 NA 5.99E-09
vg1214637266 sf1214634606 12 14637266 NA 1.33E-07