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 mr1169 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
vg1221127913 sf1221094463 12 21127913 1.68E-11 NA
vg0205081512 sf0205081509 2 5081512 9.35E-11 NA
vg1014950297 sf1014879063 10 14950297 1.03E-10 NA
vg0331256576 sf0331249461 3 31256576 2.98E-09 NA
vg0218624090 sf0218618221 2 18624090 3.97E-09 NA
vg0618463864 sf0618462867 6 18463864 1.38E-08 4.49E-06
vg0417918664 sf0417746705 4 17918664 3.85E-08 NA
vg0724513974 sf0724512980 7 24513974 4.11E-07 4.20E-06
vg0331266260 sf0331259145 3 31266260 1.16E-06 1.46E-07
vg0217446018 sf0217440148 2 17446018 8.97E-06 8.85E-07
vg0217416256 sf0217410386 2 17416256 NA 9.95E-07