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 mr1892 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
vg0701297126 sf0701296126 7 1297126 2.48E-08 NA
vg0225824157 sf0225818288 2 25824157 3.00E-08 NA
vg0904311002 sf0904310002 9 4311002 3.05E-08 3.14E-07
vg0225321246 sf0225315377 2 25321246 4.23E-08 NA
vg1112920702 sf1112457023 11 12920702 4.86E-08 NA
vg1205658688 sf1205657670 12 5658688 1.66E-06 NA
vg0200603442 sf0200603442 2 603442 2.16E-06 NA