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 mr1337 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
vg1209953191 sf1209950601 12 9953191 3.67E-08 7.56E-08
vg1104585220 sf1104581122 11 4585220 1.15E-06 6.81E-07
vg0203136151 sf0203136149 2 3136151 1.63E-06 NA
vg0401150253 sf0401145803 4 1150253 1.97E-06 6.78E-06
vg1127840259 sf1127368645 11 27840259 2.00E-06 1.47E-06
vg0420600418 sf0420428462 4 20600418 2.43E-06 5.01E-06
vg0311393570 sf0311392288 3 11393570 5.96E-06 NA
vg1104204113 sf1104200015 11 4204113 NA 3.22E-07
vg1104526300 sf1104522202 11 4526300 NA 9.25E-07
vg0706405260 sf0706404265 7 6405260 NA 1.24E-06
vg0906318181 sf0906317181 9 6318181 NA 2.93E-06