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 mr1961 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
vg1110591251 sf1110585796 11 10591251 5.42E-28 1.90E-07
vg0222673217 sf0222667348 2 22673217 7.38E-28 4.66E-10
vg0702502546 sf0702501547 7 2502546 8.09E-28 2.57E-06
vg1107745314 sf1107741059 11 7745314 4.16E-25 2.61E-06
vg0525529812 sf0525467233 5 25529812 4.55E-25 NA
vg1117963441 sf1117497299 11 17963441 3.64E-24 5.24E-07
vg0222959216 sf0222953347 2 22959216 1.81E-23 6.82E-10
vg0222735698 sf0222729829 2 22735698 NA 6.90E-07
vg0303196975 sf0303195971 3 3196975 NA 3.06E-06
vg1107481747 sf1107477492 11 7481747 NA 3.72E-06
vg0302217186 sf0302216182 3 2217186 NA 4.61E-06
vg1107484286 sf1107480031 11 7484286 NA 6.41E-06