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 mr1238 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 1.02E-68 4.10E-49
vg0105168999 sf0105167999 1 5168999 2.11E-34 2.90E-08
vg0815646521 sf0815643807 8 15646521 4.73E-33 3.15E-07
vg1124959930 sf1124493770 11 24959930 5.40E-33 1.50E-11
vg0706531615 sf0706530620 7 6531615 1.38E-32 NA
vg1125079736 sf1124613576 11 25079736 1.16E-31 8.46E-28
vg1124875808 sf1124409648 11 24875808 7.88E-30 2.82E-18
vg1124966740 sf1124500580 11 24966740 NA 1.89E-24
vg1124986792 sf1124520632 11 24986792 NA 1.13E-23
vg1124989458 sf1124523298 11 24989458 NA 3.82E-23
vg1124988847 sf1124522687 11 24988847 NA 8.63E-16
vg1125113622 sf1124647462 11 25113622 NA 7.89E-15
vg1125390548 sf1124924387 11 25390548 NA 4.91E-14
vg1125080303 sf1124614143 11 25080303 NA 5.13E-14
vg1125089512 sf1124623352 11 25089512 NA 6.15E-13
vg0328637867 sf0328630920 3 28637867 NA 2.79E-12
vg0307590023 sf0307588961 3 7590023 NA 7.32E-11
vg1125079769 sf1124613609 11 25079769 NA 1.57E-10
vg0901346489 sf0901345489 9 1346489 NA 2.05E-10
vg1124320687 sf1123854557 11 24320687 NA 2.41E-10
vg1124929928 sf1124463768 11 24929928 NA 2.73E-10
vg1125091275 sf1124625115 11 25091275 NA 3.57E-10
vg1125257504 sf1124791344 11 25257504 NA 3.74E-10
vg1125441578 sf1124975417 11 25441578 NA 4.43E-10
vg0621172424 sf0621171427 6 21172424 NA 4.44E-10
vg0717185752 sf0717184759 7 17185752 NA 7.08E-10
vg1124841437 sf1124375277 11 24841437 NA 6.95E-07