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 mr1138 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
vg0724537428 sf0724536434 7 24537428 5.42E-15 3.76E-12
vg0311637474 sf0311636192 3 11637474 2.59E-08 NA
vg1117748868 sf1117282724 11 17748868 4.02E-08 NA
vg0217994778 sf0217988909 2 17994778 6.15E-08 NA
vg0315681712 sf0315680359 3 15681712 7.35E-08 NA
vg0307374440 sf0307373438 3 7374440 9.85E-06 6.37E-07
vg0702957519 sf0702956520 7 2957519 NA 2.41E-06
vg0724473832 sf0724472838 7 24473832 NA 2.52E-06
vg0311608269 sf0311606987 3 11608269 NA 3.47E-06
vg0724481623 sf0724480629 7 24481623 NA 4.14E-06