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 mr1498 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
vg0106693749 sf0106692749 1 6693749 2.67E-59 5.33E-38
vg0106718593 sf0106717593 1 6718593 8.77E-58 1.10E-36
vg0317879120 sf0317877902 3 17879120 3.46E-35 2.57E-15
vg0112795014 sf0112793988 1 12795014 1.74E-22 4.26E-08
vg0105661905 sf0105660905 1 5661905 1.29E-20 3.66E-12
vg0229569578 sf0229563709 2 29569578 1.44E-18 NA
vg0103833171 sf0103832171 1 3833171 1.06E-16 2.05E-07
vg0224803179 sf0224797310 2 24803179 2.90E-14 2.68E-06
vg0105865082 sf0105864082 1 5865082 1.09E-13 3.19E-08
vg0106671423 sf0106670423 1 6671423 4.97E-11 4.93E-11
vg0902748143 sf0902747143 9 2748143 5.01E-09 5.89E-08
vg0105783977 sf0105782977 1 5783977 NA 2.12E-07
vg0107316579 sf0107315579 1 7316579 NA 6.12E-07
vg0114541969 sf0114540943 1 14541969 NA 1.18E-06
vg0106440529 sf0106439529 1 6440529 NA 1.39E-06
vg0525908966 sf0525846387 5 25908966 NA 1.53E-06
vg0526411540 sf0526348903 5 26411540 NA 1.72E-06
vg1206357643 sf1206356533 12 6357643 NA 2.07E-06