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 mr1449 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
vg1000405258 sf1000404258 10 405258 1.47E-07 1.47E-07
vg0302609274 sf0302608270 3 2609274 3.98E-07 3.98E-07
vg0221479912 sf0221474043 2 21479912 5.53E-07 5.53E-07
vg0130147387 sf0130146342 1 30147387 6.30E-07 6.30E-07
vg0130151904 sf0130150859 1 30151904 6.57E-07 6.57E-07
vg0303252106 sf0303251102 3 3252106 8.64E-07 8.64E-07
vg0712130030 sf0712129036 7 12130030 1.23E-06 1.23E-06
vg1117841367 sf1117375223 11 17841367 1.35E-06 1.35E-06
vg0302437930 sf0302436926 3 2437930 1.99E-06 1.99E-06
vg1209428340 sf1209425749 12 9428340 2.09E-06 2.09E-06
vg0207219076 sf0207219076 2 7219076 2.44E-06 2.44E-06
vg0107301008 sf0107300008 1 7301008 2.44E-06 2.44E-06
vg0222021907 sf0222016038 2 22021907 3.44E-06 3.44E-06
vg0900044105 sf0900043105 9 44105 3.55E-06 3.55E-06
vg0715538974 sf0715537981 7 15538974 3.90E-06 3.90E-06
vg0422143516 sf0421958398 4 22143516 4.73E-06 4.73E-06
vg0802999614 sf0802998617 8 2999614 4.92E-06 4.92E-06