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 mr1598 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
vg0918922771 sf0918921771 9 18922771 1.36E-46 1.27E-20
vg0918924003 sf0918923003 9 18924003 1.67E-46 9.34E-21
vg1102449333 sf1102445237 11 2449333 1.18E-28 9.17E-09
vg0231624655 sf0231618786 2 31624655 9.03E-26 NA
vg0327431037 sf0327424090 3 27431037 1.12E-25 NA
vg0912272939 sf0912271938 9 12272939 2.97E-25 NA
vg1005421909 sf1005438446 10 5421909 3.39E-18 2.13E-07
vg0918923523 sf0918922523 9 18923523 NA 1.03E-12
vg1102378690 sf1102374549 11 2378690 NA 1.68E-07
vg0919332322 sf0919331912 9 19332322 NA 7.54E-07
vg0917226024 sf0917225023 9 17226024 NA 7.81E-07
vg1100096982 sf1100095982 11 96982 NA 1.34E-06
vg1200902440 sf1200901440 12 902440 NA 1.45E-06
vg0919230422 sf0919230012 9 19230422 NA 1.65E-06
vg0920248805 sf0920248324 9 20248805 NA 2.29E-06
vg0918678949 sf0918677948 9 18678949 NA 3.03E-06
vg0721414343 sf0721413350 7 21414343 NA 3.44E-06