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 mr1980 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
vg1013525472 sf1013454242 10 13525472 1.69E-41 4.42E-32
vg1013579576 sf1013508346 10 13579576 2.72E-13 6.88E-07
vg1013526752 sf1013455522 10 13526752 2.71E-12 8.79E-12
vg1013346416 sf1013275186 10 13346416 5.09E-11 6.87E-07
vg1125822467 sf1125356386 11 25822467 7.18E-11 NA
vg1013767614 sf1013696383 10 13767614 2.54E-09 9.46E-07
vg1013340402 sf1013269172 10 13340402 4.39E-09 3.86E-06
vg1013412160 sf1013340930 10 13412160 1.07E-08 1.37E-06
vg0431082926 sf0430897815 4 31082926 4.60E-07 NA
vg1013500622 sf1013429392 10 13500622 NA 5.15E-08
vg0518191135 sf0518130621 5 18191135 NA 1.92E-07
vg0617019177 sf0617018180 6 17019177 NA 2.77E-06