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 mr1495 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
vg0434560709 sf0434375601 4 34560709 2.11E-10 NA
vg0108582948 sf0108581948 1 8582948 2.48E-10 2.25E-07
vg0628759426 sf0628758428 6 28759426 2.87E-10 1.98E-06
vg1007436632 sf1007452255 10 7436632 7.46E-10 NA
vg1002821112 sf1002820089 10 2821112 1.32E-09 NA
vg1002771247 sf1002770224 10 2771247 1.71E-08 NA
vg0910545581 sf0910544580 9 10545581 2.95E-08 2.53E-06
vg0432345183 sf0432160072 4 32345183 3.97E-07 3.50E-07
vg0112302656 sf0112301630 1 12302656 5.26E-07 2.16E-06
vg0224215161 sf0224209292 2 24215161 6.82E-07 1.76E-06
vg0906300837 sf0906299837 9 6300837 8.57E-07 3.50E-06
vg1008173119 sf1008101981 10 8173119 9.84E-07 NA
vg1221142592 sf1221109138 12 21142592 4.37E-06 3.92E-06
vg1110033896 sf1110028473 11 10033896 6.86E-06 4.30E-06
vg1218585338 sf1218556774 12 18585338 NA 4.32E-06