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 mr1479 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
vg1217039777 sf1217033731 12 17039777 8.07E-09 NA
vg1219189600 sf1219161070 12 19189600 1.86E-08 NA
vg1000659191 sf1000658167 10 659191 1.88E-08 NA
vg1105925054 sf1105920806 11 5925054 2.16E-08 NA
vg0130148110 sf0130147065 1 30148110 2.85E-08 NA
vg0200799535 sf0200799535 2 799535 5.74E-08 3.04E-06
vg0122411008 sf0122409963 1 22411008 1.24E-07 5.89E-06
vg0131037410 sf0131036366 1 31037410 1.62E-07 NA
vg0310177475 sf0310176391 3 10177475 3.56E-06 3.97E-07
vg0420830218 sf0420658261 4 20830218 NA 9.14E-07
vg1000843357 sf1000842333 10 843357 NA 1.25E-06