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 mr1769 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
vg0106805757 sf0106804757 1 6805757 1.06E-58 2.43E-31
vg0102388565 sf0102387565 1 2388565 5.19E-21 8.76E-08
vg0823855479 sf0823852765 8 23855479 6.16E-21 2.24E-06
vg0507524947 sf0507524889 5 7524947 9.88E-21 4.38E-06
vg0506202367 sf0506202306 5 6202367 1.01E-20 4.17E-06
vg0608142673 sf0608141674 6 8142673 1.55E-20 NA
vg1127856920 sf1127385306 11 27856920 5.05E-20 8.71E-07
vg0102410486 sf0102409486 1 2410486 1.46E-19 3.97E-08
vg0215664387 sf0215658517 2 15664387 1.04E-17 2.60E-08
vg0218246903 sf0218241034 2 18246903 2.76E-17 1.78E-06
vg0912813365 sf0912812364 9 12813365 4.50E-16 2.98E-06
vg0106608184 sf0106607184 1 6608184 NA 8.82E-07
vg0106381026 sf0106380026 1 6381026 NA 2.44E-06
vg0106681042 sf0106680042 1 6681042 NA 2.60E-06
vg1009276703 sf1009205524 10 9276703 NA 4.16E-06