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 mr1679 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
vg0722679489 sf0722678496 7 22679489 8.33E-10 NA
vg0421759361 sf0421587411 4 21759361 3.21E-08 NA
vg0906459575 sf0906458575 9 6459575 9.14E-08 NA
vg0721064561 sf0721063568 7 21064561 2.71E-07 7.58E-06
vg1216284181 sf1216281477 12 16284181 5.64E-07 4.82E-06
vg0501337655 sf0501337639 5 1337655 4.20E-06 NA
vg0215099780 sf0215093910 2 15099780 5.97E-06 NA
vg1204019355 sf1204018343 12 4019355 9.30E-06 NA
vg0511023890 sf0511023819 5 11023890 NA 3.63E-06
vg0504466784 sf0504466761 5 4466784 NA 4.62E-06
vg0711195681 sf0711194687 7 11195681 NA 4.89E-06