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 mr1398 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
vg0400775321 sf0400774321 4 775321 2.06E-08 NA
vg1127164659 sf1126693046 11 27164659 3.18E-08 NA
vg0109353965 sf0109352941 1 9353965 3.62E-08 4.56E-06
vg1216059765 sf1216057061 12 16059765 3.90E-08 NA
vg0618978160 sf0618977163 6 18978160 3.91E-08 NA
vg0920856743 sf0920856262 9 20856743 5.83E-06 NA
vg0416678941 sf0416506984 4 16678941 9.77E-06 5.66E-06
vg0621805302 sf0621804305 6 21805302 NA 1.66E-06
vg0621807445 sf0621806448 6 21807445 NA 3.02E-06
vg0711204473 sf0711203479 7 11204473 NA 3.65E-06