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 mr1166 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
vg0406833799 sf0406829244 4 6833799 1.22E-09 3.30E-07
vg0916169105 sf0916168104 9 16169105 9.97E-09 8.21E-06
vg0919713003 sf0919712593 9 19713003 1.29E-08 7.58E-06
vg0130154178 sf0130153133 1 30154178 2.97E-08 NA
vg0235115897 sf0235110028 2 35115897 2.97E-08 NA
vg0235115955 sf0235110086 2 35115955 3.31E-08 2.38E-06
vg0628103813 sf0628102815 6 28103813 5.25E-08 2.21E-06
vg0916266442 sf0916265441 9 16266442 2.43E-07 NA
vg0221948033 sf0221942164 2 21948033 3.27E-07 1.91E-06
vg0919782127 sf0919781646 9 19782127 3.68E-07 3.70E-06
vg0316217499 sf0316216147 3 16217499 6.36E-07 1.61E-06
vg0620348476 sf0620347479 6 20348476 8.30E-07 3.28E-06
vg0523054357 sf0522991798 5 23054357 5.89E-06 2.33E-06
vg0321406609 sf0321405119 3 21406609 NA 5.93E-07
vg0628386367 sf0628385369 6 28386367 NA 3.45E-06