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 mr1664 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
vg0407824993 sf0407820261 4 7824993 1.22E-07 1.22E-07
vg0123676253 sf0123675209 1 23676253 9.78E-07 9.78E-07
vg0224728169 sf0224722300 2 24728169 1.05E-06 1.05E-06
vg0408103883 sf0408099157 4 8103883 2.08E-06 2.08E-06
vg0519814183 sf0519751667 5 19814183 2.16E-06 2.16E-06
vg1213765890 sf1213763228 12 13765890 2.20E-06 2.20E-06
vg0105481161 sf0105480161 1 5481161 4.67E-06 4.67E-06
vg0411099780 sf0411090481 4 11099780 4.79E-06 4.80E-06