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 mr1691 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
vg1204622168 sf1204621156 12 4622168 3.00E-13 2.20E-10
vg0720805926 sf0720804933 7 20805926 1.77E-11 1.31E-09
vg1204623065 sf1204622053 12 4623065 5.03E-11 1.35E-08
vg0105931184 sf0105930184 1 5931184 1.33E-10 7.23E-08
vg0336193973 sf0336186899 3 36193973 4.48E-10 2.93E-07
vg1019364275 sf1019292830 10 19364275 1.57E-09 1.83E-06
vg1016349417 sf1016278193 10 16349417 2.95E-09 1.74E-06
vg0332394267 sf0332387139 3 32394267 7.55E-09 2.36E-06
vg1122414487 sf1121948358 11 22414487 1.65E-08 1.69E-06
vg1200363040 sf1200362040 12 363040 4.81E-08 3.84E-06
vg0625443240 sf0625442243 6 25443240 1.09E-07 1.96E-06
vg0721581927 sf0721580934 7 21581927 1.05E-06 5.67E-07
vg0134236787 sf0134235744 1 34236787 NA 1.52E-06
vg0804873511 sf0804872514 8 4873511 NA 3.32E-06