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 mr1620 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
vg0719051231 sf0719050238 7 19051231 4.60E-23 3.40E-19
vg0719039736 sf0719038743 7 19039736 5.93E-23 1.78E-19
vg0329561125 sf0329554165 3 29561125 8.15E-10 1.75E-07
vg0315209530 sf0315208177 3 15209530 1.56E-09 3.91E-06
vg0422276479 sf0422091361 4 22276479 7.38E-09 NA
vg0405725035 sf0405720474 4 5725035 9.18E-09 NA
vg0421592157 sf0421420207 4 21592157 2.22E-08 1.12E-06
vg0719053396 sf0719052403 7 19053396 NA 3.14E-08