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 mr1010 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
vg0434000706 sf0433815599 4 34000706 2.36E-30 8.60E-12
vg0433794465 sf0433609350 4 33794465 5.33E-30 3.24E-12
vg0136958261 sf0136957218 1 36958261 1.14E-27 9.29E-07
vg0426966163 sf0426781035 4 26966163 4.27E-27 4.48E-06
vg0521648388 sf0521585830 5 21648388 1.13E-26 NA
vg0131431344 sf0131430300 1 31431344 4.66E-26 NA
vg0137613833 sf0137612790 1 37613833 1.04E-25 5.75E-07
vg0826352073 sf0826349359 8 26352073 1.73E-25 2.81E-07
vg0235315290 sf0235309421 2 35315290 2.23E-25 2.47E-06
vg0131565087 sf0131564043 1 31565087 2.81E-25 2.09E-06
vg0428888367 sf0428703224 4 28888367 6.03E-25 5.37E-07
vg0131565701 sf0131564657 1 31565701 8.81E-25 3.54E-06
vg0304899939 sf0304898941 3 4899939 7.29E-22 NA
vg0907789558 sf0907788558 9 7789558 3.63E-20 4.09E-06
vg0433948721 sf0433763617 4 33948721 NA 1.67E-07
vg0628888899 sf0628887901 6 28888899 NA 4.37E-07
vg0915200017 sf0915199016 9 15200017 NA 1.23E-06
vg0921456034 sf0921455553 9 21456034 NA 1.68E-06
vg0902019555 sf0902018555 9 2019555 NA 6.86E-06