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 mr1317 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
vg0216966032 sf0216960162 2 16966032 6.19E-42 2.72E-23
vg0217155660 sf0217149790 2 17155660 5.90E-41 1.43E-23
vg1220336261 sf1220307703 12 20336261 4.66E-20 5.53E-11
vg1015182556 sf1015111324 10 15182556 5.14E-19 3.07E-09
vg1108225523 sf1108220133 11 8225523 2.23E-16 NA
vg1128516527 sf1127993306 11 28516527 3.25E-15 5.05E-07
vg1216728800 sf1216722754 12 16728800 2.64E-14 1.23E-06
vg0216182780 sf0216176910 2 16182780 9.93E-14 8.30E-08
vg0218850698 sf0218844829 2 18850698 1.47E-12 1.22E-08
vg0216627913 sf0216622043 2 16627913 1.16E-11 2.67E-09
vg0216764706 sf0216758836 2 16764706 1.03E-08 7.02E-07
vg0804277601 sf0804276604 8 4277601 1.12E-07 3.44E-06
vg1020178518 sf1020107016 10 20178518 2.03E-06 4.42E-06
vg0808043321 sf0808042325 8 8043321 4.05E-06 4.75E-06
vg0906775937 sf0906774937 9 6775937 4.57E-06 NA
vg1013682143 sf1013610912 10 13682143 NA 5.60E-07
vg0412563359 sf0412554069 4 12563359 NA 2.68E-06