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 mr1756 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
vg0304598567 sf0304597569 3 4598567 1.53E-13 NA
vg0503091975 sf0503091951 5 3091975 3.07E-13 NA
vg1118091589 sf1117625447 11 18091589 3.92E-13 NA
vg0818657655 sf0818654942 8 18657655 4.21E-13 NA
vg0105725060 sf0105724060 1 5725060 4.52E-13 NA
vg0106417380 sf0106416380 1 6417380 6.38E-10 NA
vg0819985140 sf0819982427 8 19985140 NA 1.95E-06
vg0608550861 sf0608549862 6 8550861 NA 2.63E-06
vg1219176479 sf1219147949 12 19176479 NA 2.96E-06
vg0413259265 sf0413249975 4 13259265 NA 3.20E-06
vg0232481318 sf0232475449 2 32481318 NA 4.19E-06