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 mr1499 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
vg0524836140 sf0524773555 5 24836140 6.72E-16 1.91E-06
vg0529415546 sf0529352901 5 29415546 2.37E-15 4.30E-07
vg0514316043 sf0514258586 5 14316043 1.03E-14 NA
vg0309145337 sf0309144273 3 9145337 1.52E-14 NA
vg0509208793 sf0509208722 5 9208793 2.40E-14 NA
vg1007992674 sf1008051562 10 7992674 2.51E-14 2.37E-06
vg0522894702 sf0522832144 5 22894702 1.33E-13 3.10E-07
vg0908903383 sf0908902382 9 8903383 2.17E-13 3.86E-06
vg0402104951 sf0402100545 4 2104951 1.14E-12 3.27E-06
vg0135017715 sf0135016672 1 35017715 4.32E-11 NA
vg0507694055 sf0507693996 5 7694055 5.02E-11 3.18E-06
vg1119435326 sf1118969014 11 19435326 NA 1.44E-06
vg0407849294 sf0407844562 4 7849294 NA 1.53E-06
vg0729687346 sf0729686354 7 29687346 NA 1.66E-06
vg0409571274 sf0409561972 4 9571274 NA 3.38E-06
vg0700497068 sf0700496068 7 497068 NA 3.65E-06