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 mr1132 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
vg1215967035 sf1215964331 12 15967035 1.53E-46 6.27E-26
vg1011512136 sf1011440955 10 11512136 1.73E-17 8.79E-07
vg0326424627 sf0326417721 3 26424627 4.89E-17 NA
vg0500829493 sf0500829475 5 829493 1.26E-15 NA
vg1212873997 sf1212871336 12 12873997 2.84E-15 5.37E-06
vg1218663003 sf1218634438 12 18663003 5.51E-14 2.47E-09
vg1215876237 sf1215873533 12 15876237 1.64E-13 1.69E-08
vg1006587700 sf1006603323 10 6587700 4.05E-13 9.76E-09
vg1208048502 sf1208045908 12 8048502 8.35E-12 1.03E-08
vg1022588644 sf1022517118 10 22588644 1.31E-11 8.02E-11
vg1011512046 sf1011440865 10 11512046 2.14E-10 3.62E-07
vg1215852700 sf1215849996 12 15852700 NA 4.26E-11
vg1216463200 sf1216460493 12 16463200 NA 1.83E-07
vg0433192266 sf0433007154 4 33192266 NA 3.91E-07
vg0612563711 sf0612562712 6 12563711 NA 4.89E-07
vg1215551588 sf1215548885 12 15551588 NA 7.68E-07
vg1209876216 sf1209873626 12 9876216 NA 7.69E-07
vg1206197673 sf1206196564 12 6197673 NA 1.01E-06
vg0616969932 sf0616968935 6 16969932 NA 2.33E-06
vg0715496678 sf0715495685 7 15496678 NA 3.75E-06