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 mr1304 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
vg0521675477 sf0521612919 5 21675477 3.76E-22 NA
vg0124366565 sf0124365521 1 24366565 1.46E-21 NA
vg0310767670 sf0310766586 3 10767670 2.92E-21 NA
vg0528815688 sf0528753043 5 28815688 1.40E-20 NA
vg0827197288 sf0827194574 8 27197288 2.10E-20 NA
vg0726437652 sf0726436658 7 26437652 2.27E-20 1.27E-08
vg1218127830 sf1218099266 12 18127830 3.05E-18 NA
vg0917631829 sf0917630828 9 17631829 NA 4.88E-08
vg1001435000 sf1001433977 10 1435000 NA 2.03E-06
vg1001216315 sf1001215292 10 1216315 NA 2.48E-06
vg0608122121 sf0608121122 6 8122121 NA 4.18E-06
vg1128511488 sf1127988267 11 28511488 NA 4.55E-06