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 mr1180 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
vg0222739831 sf0222733962 2 22739831 6.86E-15 3.42E-13
vg0805562872 sf0805561875 8 5562872 5.01E-13 NA
vg0726946907 sf0726945913 7 26946907 1.95E-12 NA
vg0808948492 sf0808947496 8 8948492 6.42E-12 NA
vg0912077331 sf0912076330 9 12077331 1.34E-11 NA
vg0805546102 sf0805545105 8 5546102 2.63E-11 2.86E-06
vg1005684375 sf1005700913 10 5684375 2.00E-10 NA
vg0718667525 sf0718666532 7 18667525 1.20E-09 NA
vg0326817228 sf0326810282 3 26817228 7.85E-07 NA
vg0222883605 sf0222877736 2 22883605 NA 2.18E-06
vg0707162876 sf0707161881 7 7162876 NA 4.50E-06
vg0721894601 sf0721893608 7 21894601 NA 4.93E-06