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 mr1220 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
vg0324965295 sf0324963375 3 24965295 4.95E-11 1.18E-07
vg0435177919 sf0434992800 4 35177919 5.37E-10 1.40E-06
vg0428287310 sf0428102173 4 28287310 1.89E-09 1.70E-06
vg0713426232 sf0713425239 7 13426232 3.34E-09 4.18E-07
vg0131794141 sf0131793097 1 31794141 4.45E-09 6.63E-06
vg0700897980 sf0700896980 7 897980 8.35E-09 3.24E-06
vg0721047449 sf0721046456 7 21047449 6.69E-08 3.99E-06
vg0509233251 sf0509233180 5 9233251 7.66E-07 1.90E-06
vg0125628571 sf0125627527 1 25628571 8.39E-06 2.09E-07
vg0207729665 sf0207729664 2 7729665 NA 2.27E-06
vg0223248427 sf0223242558 2 23248427 NA 3.33E-06