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 mr1577 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
vg1216002562 sf1215999858 12 16002562 5.54E-11 3.03E-07
vg1214831971 sf1214829312 12 14831971 4.05E-10 1.85E-07
vg1210551107 sf1210548520 12 10551107 3.38E-09 NA
vg1208187601 sf1208185007 12 8187601 4.60E-09 NA
vg1218172024 sf1218143460 12 18172024 5.17E-09 6.37E-06
vg0800137751 sf0800136751 8 137751 1.97E-08 4.42E-07
vg0800121546 sf0800120546 8 121546 3.50E-08 8.30E-07
vg1209231884 sf1209229293 12 9231884 1.39E-07 4.62E-06
vg1121965345 sf1121499216 11 21965345 5.65E-07 NA
vg0807428797 sf0807427802 8 7428797 6.04E-06 NA
vg0500854181 sf0500854163 5 854181 9.21E-06 NA
vg0503447917 sf0503447894 5 3447917 NA 4.40E-07
vg1014019485 sf1013948251 10 14019485 NA 2.00E-06
vg0610852428 sf0610851429 6 10852428 NA 3.66E-06