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 mr1095 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
vg0222743508 sf0222737639 2 22743508 7.11E-71 4.06E-35
vg0222724011 sf0222718142 2 22724011 2.51E-70 2.43E-35
vg0906971590 sf0906970590 9 6971590 1.49E-30 NA
vg1201304868 sf1201303868 12 1304868 4.69E-29 NA
vg0525484604 sf0525422025 5 25484604 4.70E-29 NA
vg1008227206 sf1008156068 10 8227206 2.97E-27 NA
vg0524971409 sf0524908824 5 24971409 1.59E-26 2.55E-06
vg1201913624 sf1201912622 12 1913624 3.32E-26 4.27E-06
vg0222679274 sf0222673405 2 22679274 7.53E-23 1.63E-06
vg0222725003 sf0222719134 2 22725003 6.55E-20 6.26E-13
vg0222817468 sf0222811599 2 22817468 NA 7.57E-09
vg0222629829 sf0222623960 2 22629829 NA 2.95E-08
vg0223811992 sf0223783239 2 23811992 NA 4.11E-08
vg0224958355 sf0224952486 2 24958355 NA 5.28E-08
vg0524972451 sf0524909866 5 24972451 NA 1.06E-07
vg0224793596 sf0224787727 2 24793596 NA 4.40E-07
vg0224676560 sf0224670691 2 24676560 NA 1.12E-06
vg0224788519 sf0224782650 2 24788519 NA 1.84E-06