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 mr1043 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
vg1105921472 sf1105917224 11 5921472 2.18E-12 5.87E-06
vg0431443109 sf0431258007 4 31443109 2.24E-10 NA
vg0919811754 sf0919811273 9 19811754 2.33E-10 NA
vg0131497144 sf0131496100 1 31497144 3.91E-10 NA
vg1105906134 sf1105901886 11 5906134 1.11E-09 2.10E-06
vg1219172886 sf1219144356 12 19172886 1.35E-09 NA
vg0617895267 sf0617894270 6 17895267 1.82E-09 4.25E-06
vg0114524304 sf0114523278 1 14524304 3.40E-09 3.55E-06
vg0413440235 sf0413430949 4 13440235 1.38E-08 5.01E-07
vg0715703952 sf0715702959 7 15703952 8.92E-08 3.96E-06
vg0314017083 sf0314015800 3 14017083 1.18E-07 2.87E-06
vg0319980220 sf0319978731 3 19980220 1.01E-06 3.81E-06
vg0141729776 sf0141728733 1 41729776 1.02E-06 NA
vg0117203916 sf0117202870 1 17203916 NA 2.05E-06
vg0520358656 sf0520296129 5 20358656 NA 2.66E-06
vg0614629276 sf0614628277 6 14629276 NA 3.45E-06