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 mr1063 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
vg1010658374 sf1010587195 10 10658374 7.56E-59 NA
vg0424962676 sf0424777537 4 24962676 1.05E-58 NA
vg1201345685 sf1201344685 12 1345685 2.81E-58 8.30E-06
vg1201368119 sf1201367119 12 1368119 2.87E-58 3.71E-06
vg1201368089 sf1201367089 12 1368089 4.13E-58 NA
vg0233415607 sf0233409738 2 33415607 1.56E-57 NA
vg0303086517 sf0303085513 3 3086517 2.20E-57 NA
vg1020723356 sf1020651835 10 20723356 9.97E-55 NA
vg0600691732 sf0600690733 6 691732 NA 1.53E-07
vg0222725881 sf0222720012 2 22725881 NA 3.70E-07
vg1216930858 sf1216924812 12 16930858 NA 3.14E-06
vg0222730480 sf0222724611 2 22730480 NA 3.25E-06
vg0600570367 sf0600569368 6 570367 NA 3.86E-06