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
vg0336109020 sf0336101946 3 36109020 1.46E-09 8.01E-09
vg0336102786 sf0336095712 3 36102786 6.81E-09 4.77E-09
vg1105448751 sf1105444502 11 5448751 1.40E-08 4.17E-06
vg0234423363 sf0234417494 2 34423363 1.44E-08 3.82E-06
vg0204866143 sf0204866140 2 4866143 2.96E-08 NA
vg0336048686 sf0336041555 3 36048686 3.76E-08 5.77E-08
vg0201096822 sf0201096822 2 1096822 3.11E-06 NA
vg0233749871 sf0233744002 2 33749871 3.20E-06 NA