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 mr1088 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
vg0719011406 sf0719010413 7 19011406 3.10E-96 1.15E-23
vg0719088617 sf0719087624 7 19088617 6.06E-74 1.01E-23
vg0215987097 sf0215981227 2 15987097 2.75E-70 NA
vg0917782314 sf0917781313 9 17782314 4.19E-70 NA
vg1201568993 sf1201567993 12 1568993 1.38E-69 NA
vg1010655735 sf1010584556 10 10655735 3.13E-68 NA
vg1107675284 sf1107671029 11 7675284 1.31E-63 4.24E-06
vg0719304067 sf0719303074 7 19304067 5.53E-58 2.79E-13
vg0719091461 sf0719090468 7 19091461 NA 1.10E-20
vg0719153604 sf0719152611 7 19153604 NA 2.99E-10
vg0718955684 sf0718954691 7 18955684 NA 1.00E-09
vg0718996077 sf0718995084 7 18996077 NA 5.86E-09
vg0719140779 sf0719139786 7 19140779 NA 1.12E-08
vg0719071513 sf0719070520 7 19071513 NA 1.66E-08
vg0216352293 sf0216346423 2 16352293 NA 4.13E-08
vg0719347879 sf0719346886 7 19347879 NA 6.28E-08
vg0719466615 sf0719465622 7 19466615 NA 8.33E-08
vg0719346699 sf0719345706 7 19346699 NA 1.55E-07
vg0315366561 sf0315365208 3 15366561 NA 1.86E-07
vg0315270004 sf0315268651 3 15270004 NA 3.88E-07
vg1007933835 sf1007949445 10 7933835 NA 4.33E-07
vg0206372400 sf0206372400 2 6372400 NA 8.98E-07
vg0216328549 sf0216322679 2 16328549 NA 9.33E-07
vg0235249589 sf0235243720 2 35249589 NA 1.06E-06
vg0228211407 sf0228205538 2 28211407 NA 2.48E-06
vg0804346142 sf0804345145 8 4346142 NA 2.75E-06
vg1217503545 sf1217497500 12 17503545 NA 4.56E-06