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 mr1248 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
vg1113972556 sf1113508877 11 13972556 3.86E-12 NA
vg1015866435 sf1015795205 10 15866435 4.17E-12 NA
vg1110343275 sf1110337852 11 10343275 6.11E-12 NA
vg0120180517 sf0120179472 1 20180517 7.54E-12 NA
vg1105861771 sf1105857523 11 5861771 7.71E-12 1.25E-06
vg1105880412 sf1105876164 11 5880412 1.21E-11 1.05E-06
vg1105927518 sf1105923270 11 5927518 1.76E-11 1.02E-06
vg0413568072 sf0413558786 4 13568072 1.12E-10 NA