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 mr1789 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
vg0401800475 sf0401796070 4 1800475 2.65E-08 5.02E-06
vg0403204227 sf0403199830 4 3204227 5.78E-08 NA
vg1008062862 sf1007981375 10 8062862 8.55E-08 NA
vg0800884996 sf0800883998 8 884996 2.86E-07 2.50E-06
vg0404418363 sf0404413967 4 4418363 4.09E-07 NA
vg0111585803 sf0111584777 1 11585803 9.35E-07 3.86E-06
vg0711096071 sf0711095077 7 11096071 1.96E-06 2.58E-06
vg0702351176 sf0702350177 7 2351176 2.25E-06 1.29E-06
vg0330758731 sf0330751618 3 30758731 2.68E-06 NA
vg1201963101 sf1201962099 12 1963101 NA 1.00E-06
vg0517802011 sf0517741497 5 17802011 NA 2.27E-06