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 mr1282 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
vg0223637476 sf0223631607 2 23637476 2.08E-07 2.08E-07
vg0709984451 sf0709983457 7 9984451 1.32E-06 1.32E-06
vg0627798787 sf0627797789 6 27798787 1.98E-06 1.98E-06
vg0421078392 sf0420906445 4 21078392 2.20E-06 2.20E-06
vg0817748584 sf0817745871 8 17748584 2.61E-06 2.61E-06
vg0621702300 sf0621701303 6 21702300 3.62E-06 3.62E-06
vg0805895531 sf0805894534 8 5895531 3.84E-06 3.84E-06
vg1215802194 sf1215799491 12 15802194 5.08E-06 5.08E-06
vg0421054354 sf0420882409 4 21054354 6.66E-06 6.66E-06