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 mr1520 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
vg0113820276 sf0113819250 1 13820276 3.79E-08 NA
vg0414190693 sf0414181409 4 14190693 4.30E-08 NA
vg0141996307 sf0141995264 1 41996307 4.50E-08 NA
vg0718960888 sf0718959895 7 18960888 4.70E-08 NA
vg0719274985 sf0719273992 7 19274985 8.48E-08 NA
vg1123192315 sf1122726186 11 23192315 1.91E-07 2.18E-06
vg0922458193 sf0922457712 9 22458193 6.56E-07 4.99E-06
vg0922425823 sf0922425342 9 22425823 1.28E-06 3.23E-06
vg0722002330 sf0722001337 7 22002330 1.51E-06 4.66E-06