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 mr1337 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
vg0424181194 sf0423996055 4 24181194 4.41E-08 4.41E-08
vg1124705653 sf1124239493 11 24705653 9.98E-08 9.98E-08
vg0704864945 sf0704863946 7 4864945 3.10E-07 3.10E-07
vg0421384856 sf0421212909 4 21384856 3.36E-07 3.36E-07
vg0516508609 sf0516451091 5 16508609 7.31E-07 7.31E-07
vg1225484489 sf1225450884 12 25484489 1.43E-06 1.43E-06
vg0223522667 sf0223516798 2 23522667 1.66E-06 1.66E-06
vg0421031577 sf0420859630 4 21031577 1.72E-06 1.72E-06
vg0420718113 sf0420546156 4 20718113 2.31E-06 2.31E-06
vg0403140954 sf0403136557 4 3140954 2.54E-06 2.54E-06
vg1224447613 sf1224414066 12 24447613 3.15E-06 3.15E-06
vg0909710935 sf0909709934 9 9710935 3.41E-06 3.41E-06
vg0921004343 sf0921003862 9 21004343 3.70E-06 3.70E-06
vg0607659813 sf0607658814 6 7659813 3.89E-06 3.89E-06
vg1000491820 sf1000490796 10 491820 4.02E-06 4.02E-06
vg0403204105 sf0403199708 4 3204105 4.04E-06 4.04E-06
vg0400019945 sf0400018945 4 19945 4.27E-06 4.27E-06
vg0801344289 sf0801343291 8 1344289 4.76E-06 4.76E-06
vg0515278523 sf0515221064 5 15278523 9.85E-06 9.85E-06