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 mr1828 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
vg0525976899 sf0525914319 5 25976899 3.27E-21 3.23E-14
vg0526224458 sf0526161822 5 26224458 2.88E-20 1.19E-14
vg0528881504 sf0528818859 5 28881504 1.30E-12 4.53E-07
vg0528998640 sf0528935995 5 28998640 1.50E-12 2.19E-07
vg1128432615 sf1127909394 11 28432615 4.56E-12 4.32E-07
vg1102424189 sf1102420093 11 2424189 8.60E-12 NA
vg0528921697 sf0528859052 5 28921697 1.06E-11 6.25E-07
vg1118572833 sf1118106643 11 18572833 7.61E-11 NA
vg0525973696 sf0525911116 5 25973696 7.03E-09 4.08E-06
vg0330774928 sf0330767815 3 30774928 1.75E-07 1.21E-06
vg0514453167 sf0514395710 5 14453167 NA 1.44E-06
vg0820991239 sf0820988526 8 20991239 NA 2.76E-06