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 mr1374 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
vg0332529432 sf0332522305 3 32529432 5.76E-07 5.76E-07
vg0911098439 sf0911097438 9 11098439 6.82E-07 6.82E-07
vg0808453559 sf0808452563 8 8453559 8.25E-07 8.25E-07
vg1223792549 sf1223759002 12 23792549 1.53E-06 1.53E-06
vg1219111880 sf1219083316 12 19111880 2.98E-06 2.98E-06
vg0808455654 sf0808454658 8 8455654 3.57E-06 3.57E-06
vg1110611200 sf1110605745 11 10611200 4.85E-06 4.85E-06
vg0725159987 sf0725158993 7 25159987 8.19E-06 8.19E-06