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 mr1873 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
vg0506946112 sf0506946054 5 6946112 2.99E-53 2.30E-12
vg0215273039 sf0215267169 2 15273039 6.03E-45 NA
vg0827722509 sf0827719795 8 27722509 6.05E-45 NA
vg0921849758 sf0921849277 9 21849758 6.27E-45 NA
vg0226024465 sf0226018596 2 26024465 2.08E-44 NA
vg0427936017 sf0427750880 4 27936017 6.68E-41 3.14E-07
vg0427867301 sf0427682163 4 27867301 8.54E-41 3.80E-08
vg0500459100 sf0500459100 5 459100 NA 2.37E-06
vg1218047316 sf1218018752 12 18047316 NA 3.80E-06
vg0818666272 sf0818663559 8 18666272 NA 6.85E-06