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 mr1757 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
vg0705477376 sf0705476377 7 5477376 1.24E-13 3.82E-11
vg0907387974 sf0907386974 9 7387974 1.52E-12 2.17E-08
vg1120137948 sf1119671870 11 20137948 7.19E-12 NA
vg0129126261 sf0129125216 1 29126261 2.76E-11 3.77E-06
vg0602753568 sf0602752569 6 2753568 3.68E-11 5.83E-09
vg0129128111 sf0129127066 1 29128111 4.81E-11 1.87E-06
vg0729061858 sf0729060866 7 29061858 1.48E-10 2.78E-07
vg0402346536 sf0402342131 4 2346536 2.40E-10 4.06E-08
vg0402462870 sf0402458468 4 2462870 2.82E-10 9.07E-06
vg0609611196 sf0609610197 6 9611196 4.76E-10 3.04E-06
vg0608141426 sf0608140427 6 8141426 1.20E-09 1.44E-06
vg0308843941 sf0308842879 3 8843941 1.32E-09 1.75E-06
vg0135156282 sf0135155239 1 35156282 2.43E-07 1.50E-06
vg1128827572 sf1128304351 11 28827572 4.64E-07 7.67E-07
vg0124700675 sf0124699631 1 24700675 5.14E-06 NA