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 mr1969 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
vg0701930997 sf0701929998 7 1930997 3.86E-22 NA
vg0404341374 sf0404336979 4 4341374 1.07E-21 NA
vg1217066010 sf1217059965 12 17066010 5.22E-21 NA
vg0528026525 sf0527963880 5 28026525 5.62E-20 NA
vg0601564965 sf0601563966 6 1564965 1.46E-19 NA
vg0405865352 sf0405860793 4 5865352 2.52E-17 3.33E-06
vg1020708879 sf1020637358 10 20708879 1.30E-15 2.33E-07
vg0420830788 sf0420658831 4 20830788 NA 3.21E-07
vg0712988935 sf0712987942 7 12988935 NA 2.35E-06
vg0401199285 sf0401194835 4 1199285 NA 2.84E-06
vg1003735001 sf1003733978 10 3735001 NA 2.88E-06
vg0128125660 sf0128124616 1 28125660 NA 2.92E-06
vg0430611294 sf0430426169 4 30611294 NA 3.17E-06
vg0520332453 sf0520269926 5 20332453 NA 5.97E-06
vg0414518378 sf0414509092 4 14518378 NA 8.96E-06