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 mr1148 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
vg0222741535 sf0222735666 2 22741535 3.54E-49 2.94E-19
vg0213988415 sf0213982545 2 13988415 8.09E-33 NA
vg1223702973 sf1223669426 12 23702973 6.64E-32 NA
vg1202240785 sf1202239784 12 2240785 1.32E-31 NA
vg0626471591 sf0626470594 6 26471591 1.43E-31 NA
vg0130667376 sf0130666332 1 30667376 NA 4.99E-10
vg0130832570 sf0130831526 1 30832570 NA 6.49E-10
vg0222567385 sf0222561516 2 22567385 NA 6.89E-08
vg0611421749 sf0611420750 6 11421749 NA 1.61E-07
vg0223507983 sf0223502114 2 23507983 NA 2.84E-06
vg0224252015 sf0224246146 2 24252015 NA 3.41E-06
vg1202046442 sf1202045440 12 2046442 NA 3.42E-06