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 mr1633 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
vg1214682389 sf1214679728 12 14682389 2.79E-08 1.73E-06
vg1206482579 sf1206481469 12 6482579 1.44E-07 3.35E-06
vg0517668715 sf0517608356 5 17668715 1.92E-07 4.51E-06
vg1215126327 sf1215123663 12 15126327 1.56E-06 NA
vg0908229421 sf0908228421 9 8229421 2.23E-06 4.85E-06
vg0129442068 sf0129441023 1 29442068 3.57E-06 NA
vg0805900956 sf0805899959 8 5900956 NA 2.43E-07
vg0505749457 sf0505749395 5 5749457 NA 1.16E-06
vg0714140419 sf0714139426 7 14140419 NA 4.03E-06