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 mr1531 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
vg0507040260 sf0507040202 5 7040260 8.58E-25 1.09E-10
vg0331879544 sf0331872421 3 31879544 1.96E-18 NA
vg0722474111 sf0722473118 7 22474111 5.88E-18 NA
vg0423901663 sf0423716522 4 23901663 1.14E-17 NA
vg0141729761 sf0141728718 1 41729761 2.51E-17 NA
vg0507169486 sf0507169428 5 7169486 NA 3.25E-08
vg0321841885 sf0321840395 3 21841885 NA 4.22E-07
vg0212545067 sf0212545063 2 12545067 NA 1.63E-06
vg0113876121 sf0113875095 1 13876121 NA 2.11E-06
vg1122327568 sf1121861439 11 22327568 NA 3.89E-06
vg0504422466 sf0504422443 5 4422466 NA 5.77E-06