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 mr1080 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
vg0406562314 sf0406557757 4 6562314 3.20E-16 3.76E-11
vg0406527932 sf0406523375 4 6527932 5.97E-15 1.18E-10
vg1016565386 sf1016494159 10 16565386 5.92E-10 1.42E-06
vg0722687147 sf0722686154 7 22687147 5.22E-08 NA
vg0722626782 sf0722625789 7 22626782 6.33E-08 4.13E-06
vg0431611699 sf0431426594 4 31611699 7.25E-08 7.91E-06
vg0823019901 sf0823017188 8 23019901 7.35E-08 NA
vg0911597491 sf0911596490 9 11597491 1.13E-06 2.28E-07
vg0619717218 sf0619716221 6 19717218 1.54E-06 4.53E-06
vg0817943383 sf0817940670 8 17943383 NA 2.93E-06