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 mr1549 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 1.58E-17 2.02E-15
vg0729061858 sf0729060866 7 29061858 3.71E-13 3.37E-10
vg0907387974 sf0907386974 9 7387974 3.65E-12 1.02E-07
vg1020589936 sf1020518415 10 20589936 5.99E-12 1.74E-07
vg0602753568 sf0602752569 6 2753568 6.93E-12 2.60E-09
vg0105586222 sf0105585222 1 5586222 9.62E-12 4.19E-07
vg0129128700 sf0129127655 1 29128700 3.12E-11 3.56E-07
vg0608132926 sf0608131927 6 8132926 3.61E-11 3.76E-08
vg1127976664 sf1127505050 11 27976664 1.62E-10 8.39E-07
vg0601369122 sf0601368123 6 1369122 1.89E-10 1.21E-06
vg0308843941 sf0308842879 3 8843941 1.94E-10 2.70E-07
vg0419005856 sf0418833898 4 19005856 2.96E-10 2.56E-07
vg0909518112 sf0909517111 9 9518112 4.98E-10 6.03E-06
vg1000480049 sf1000479025 10 480049 6.97E-10 6.32E-07
vg0402346536 sf0402342131 4 2346536 1.14E-09 1.44E-07
vg0423691960 sf0423506817 4 23691960 1.22E-09 2.73E-07
vg1011837474 sf1011766289 10 11837474 6.46E-09 8.25E-07
vg0412960952 sf0412951663 4 12960952 9.82E-09 1.04E-07
vg0406137915 sf0406133355 4 6137915 3.06E-08 1.05E-06
vg0500777407 sf0500777389 5 777407 5.58E-07 NA
vg0100966110 sf0100965110 1 966110 1.25E-06 1.39E-06
vg0404559892 sf0404555495 4 4559892 1.45E-06 1.09E-06