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 mr1448 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
vg0234891437 sf0234885568 2 34891437 3.35E-39 3.26E-06
vg0235259448 sf0235253579 2 35259448 1.55E-38 3.62E-07
vg0232222921 sf0232217052 2 32222921 4.59E-36 NA
vg0729587167 sf0729586175 7 29587167 8.74E-36 NA
vg0113441758 sf0113440732 1 13441758 1.11E-35 NA
vg0206377668 sf0206377668 2 6377668 1.12E-35 NA
vg0305073222 sf0305072224 3 5073222 8.90E-35 NA
vg0123784208 sf0123783164 1 23784208 NA 7.73E-07
vg0235323589 sf0235317720 2 35323589 NA 1.85E-06
vg1122472768 sf1122006639 11 22472768 NA 2.84E-06
vg0222716080 sf0222710211 2 22716080 NA 3.15E-06
vg1012431468 sf1012360283 10 12431468 NA 3.43E-06
vg1021493840 sf1021422317 10 21493840 NA 8.60E-06