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 mr1841 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 1.87E-21 1.36E-21
vg1124991220 sf1124525060 11 24991220 2.12E-09 1.28E-11
vg1124875808 sf1124409648 11 24875808 3.12E-08 9.27E-11
vg1124914537 sf1124448377 11 24914537 8.80E-08 4.55E-12
vg1125050424 sf1124584264 11 25050424 1.09E-07 1.62E-06
vg1125087812 sf1124621652 11 25087812 1.14E-06 4.17E-08
vg1125022392 sf1124556232 11 25022392 1.66E-06 2.09E-06
vg1125545020 sf1125078859 11 25545020 3.80E-06 4.44E-06
vg0223432768 sf0223426899 2 23432768 5.16E-06 NA
vg0208320880 sf0208320879 2 8320880 NA 4.11E-07
vg1124931687 sf1124465527 11 24931687 NA 3.58E-06
vg0506420059 sf0506419999 5 6420059 NA 4.67E-06