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 mr1675 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 2.63E-22 NA
vg0701930997 sf0701929998 7 1930997 6.74E-22 NA
vg1217066010 sf1217059965 12 17066010 1.96E-21 NA
vg0528026525 sf0527963880 5 28026525 8.92E-21 NA
vg0113904382 sf0113903356 1 13904382 4.42E-20 NA
vg0405865352 sf0405860793 4 5865352 2.16E-17 3.86E-06
vg0620203384 sf0620202387 6 20203384 4.49E-17 3.53E-06
vg0100490718 sf0100489718 1 490718 4.62E-16 NA
vg1020708879 sf1020637358 10 20708879 1.28E-15 1.01E-06
vg0430611290 sf0430426165 4 30611290 NA 1.92E-06
vg0420830788 sf0420658831 4 20830788 NA 2.07E-06
vg0414518378 sf0414509092 4 14518378 NA 4.99E-06
vg1003735001 sf1003733978 10 3735001 NA 8.53E-06