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 mr1407 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
vg0721340090 sf0721339097 7 21340090 2.24E-09 6.75E-06
vg1214365279 sf1214362619 12 14365279 3.42E-09 3.31E-07
vg0821970212 sf0821967499 8 21970212 1.20E-08 NA
vg0808447137 sf0808446141 8 8447137 1.90E-08 NA
vg1217635489 sf1217629444 12 17635489 3.19E-08 NA
vg0119703755 sf0119702710 1 19703755 8.98E-08 4.68E-06
vg1127100023 sf1126628410 11 27100023 1.38E-07 8.82E-06
vg1215123131 sf1215120467 12 15123131 4.84E-07 3.42E-06
vg0815304114 sf0815301400 8 15304114 NA 5.36E-06