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 mr1846 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
vg0407271283 sf0407266553 4 7271283 1.34E-33 8.94E-12
vg0411377590 sf0411368293 4 11377590 1.39E-33 4.93E-13
vg0411404313 sf0411395016 4 11404313 3.66E-33 3.29E-14
vg0407262262 sf0407257532 4 7262262 4.08E-29 4.71E-14
vg0414021996 sf0414012711 4 14021996 2.69E-26 6.49E-08
vg0614459942 sf0614458943 6 14459942 2.18E-23 4.43E-07
vg0812791309 sf0812789134 8 12791309 2.26E-22 3.58E-08
vg0905315058 sf0905314058 9 5315058 4.62E-17 1.39E-06
vg1110033720 sf1110028297 11 10033720 3.45E-14 1.20E-06
vg0217778549 sf0217772680 2 17778549 1.01E-08 NA
vg0411635886 sf0411626592 4 11635886 2.74E-08 3.28E-06
vg0332994931 sf0332987801 3 32994931 NA 2.61E-07
vg0311297778 sf0311296496 3 11297778 NA 5.55E-07
vg0209213128 sf0209213126 2 9213128 NA 5.03E-06