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 mr1667 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
vg1125464486 sf1124998325 11 25464486 4.45E-21 2.79E-13
vg0713261979 sf0713260986 7 13261979 2.43E-16 9.45E-09
vg0612546146 sf0612545147 6 12546146 1.02E-12 1.26E-06
vg1015985151 sf1015913923 10 15985151 8.41E-10 2.15E-06
vg1125800615 sf1125334536 11 25800615 1.40E-09 2.27E-06
vg1125797847 sf1125331768 11 25797847 1.79E-09 1.30E-06
vg1008033563 sf1008010674 10 8033563 2.75E-09 1.70E-06
vg1126344361 sf1125872774 11 26344361 2.40E-08 9.97E-07
vg1126259017 sf1125787430 11 26259017 3.37E-08 2.09E-06
vg0817495758 sf0817493044 8 17495758 6.07E-08 1.14E-06
vg1003260501 sf1003259478 10 3260501 6.47E-08 4.19E-06
vg1127770033 sf1127298419 11 27770033 1.23E-07 4.53E-06
vg0434378375 sf0434193269 4 34378375 NA 3.94E-06
vg0726230011 sf0726229017 7 26230011 NA 4.50E-06