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 mr1365 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
vg1013275525 sf1013204295 10 13275525 1.45E-13 9.93E-10
vg0525124572 sf0525061987 5 25124572 5.23E-11 4.11E-07
vg0529106995 sf0529044350 5 29106995 2.69E-10 2.32E-06
vg1202159597 sf1202158595 12 2159597 3.17E-10 3.08E-06
vg1202046442 sf1202045440 12 2046442 4.49E-10 3.03E-06
vg0702123213 sf0702122214 7 2123213 6.85E-10 4.86E-06
vg0434853783 sf0434668674 4 34853783 1.27E-09 3.81E-06
vg0420839533 sf0420667576 4 20839533 3.00E-08 6.90E-08
vg1013263857 sf1013192627 10 13263857 NA 2.46E-06