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 mr1008 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
vg0133229453 sf0133228409 1 33229453 5.90E-41 7.17E-25
vg0133223996 sf0133222952 1 33223996 2.27E-35 1.77E-28
vg0135024184 sf0135023141 1 35024184 4.19E-15 3.19E-10
vg0133576355 sf0133575311 1 33576355 3.66E-14 5.93E-07
vg0135405957 sf0135404914 1 35405957 4.99E-14 5.04E-10
vg0133231306 sf0133230262 1 33231306 6.94E-14 1.54E-11
vg0133426880 sf0133425836 1 33426880 1.16E-13 2.11E-07
vg0133434075 sf0133433031 1 33434075 1.79E-13 1.54E-09
vg0135425377 sf0135424334 1 35425377 1.14E-12 8.60E-08
vg0133830553 sf0133829509 1 33830553 1.65E-12 6.24E-09
vg0130814504 sf0130813460 1 30814504 3.30E-12 1.54E-07
vg0133434063 sf0133433019 1 33434063 3.55E-12 5.50E-07
vg0132643720 sf0132642676 1 32643720 1.67E-11 1.89E-08
vg0135032175 sf0135031132 1 35032175 3.70E-11 3.43E-07
vg0133400564 sf0133399520 1 33400564 6.12E-11 1.52E-08
vg0134951253 sf0134950210 1 34951253 1.37E-10 1.08E-09
vg0131534483 sf0131533439 1 31534483 1.93E-10 7.70E-07
vg0133789019 sf0133787975 1 33789019 7.28E-10 1.06E-06
vg0131429542 sf0131428498 1 31429542 2.74E-09 5.50E-07
vg0921457298 sf0921456817 9 21457298 7.46E-09 NA
vg0134869973 sf0134868930 1 34869973 4.89E-08 5.95E-08
vg0712961657 sf0712960664 7 12961657 5.36E-06 1.33E-07
vg0922310318 sf0922309837 9 22310318 NA 7.30E-07
vg0330192805 sf0330185844 3 30192805 NA 1.08E-06
vg1121732413 sf1121266290 11 21732413 NA 1.11E-06