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 mr1059 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
vg0404341374 sf0404336979 4 4341374 1.75E-22 NA
vg0701923849 sf0701922850 7 1923849 2.48E-21 NA
vg0113904382 sf0113903356 1 13904382 3.48E-20 NA
vg0919811177 sf0919810696 9 19811177 4.29E-20 NA
vg0133158489 sf0133157445 1 33158489 6.09E-20 NA
vg1020708879 sf1020637358 10 20708879 2.05E-16 7.64E-07
vg0604924928 sf0604923929 6 4924928 2.03E-15 NA
vg0430611290 sf0430426165 4 30611290 NA 1.18E-06
vg0420830218 sf0420658261 4 20830218 NA 1.52E-06
vg0400052458 sf0400051458 4 52458 NA 1.95E-06
vg0434885431 sf0434700321 4 34885431 NA 2.41E-06