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 mr1002 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
vg1207803628 sf1207801034 12 7803628 1.57E-31 4.63E-28
vg1207984922 sf1207982328 12 7984922 1.38E-25 2.80E-15
vg1207825767 sf1207823173 12 7825767 5.12E-24 9.37E-16
vg1208087778 sf1208085184 12 8087778 2.65E-21 2.69E-13
vg1208517760 sf1208515167 12 8517760 1.65E-18 2.87E-10
vg0122800847 sf0122799803 1 22800847 5.99E-18 3.32E-08
vg0131734945 sf0131733901 1 31734945 6.39E-18 NA
vg0819131363 sf0819128650 8 19131363 2.70E-17 3.71E-08
vg1203754517 sf1203753516 12 3754517 3.06E-17 2.35E-08
vg0805899713 sf0805898716 8 5899713 7.67E-17 2.62E-07
vg0335045132 sf0335038002 3 35045132 2.84E-16 1.15E-08
vg1207886389 sf1207883795 12 7886389 4.98E-16 3.50E-16
vg1207900135 sf1207897541 12 7900135 5.45E-16 9.09E-20
vg1209894319 sf1209891729 12 9894319 2.06E-15 2.56E-07
vg0727554901 sf0727553907 7 27554901 4.17E-15 1.73E-07
vg1216542519 sf1216539812 12 16542519 2.71E-13 4.56E-07
vg0332136561 sf0332129438 3 32136561 8.62E-13 6.15E-07
vg0727574396 sf0727573402 7 27574396 1.12E-09 6.24E-08
vg1209262766 sf1209260175 12 9262766 NA 2.70E-10
vg0302493103 sf0302492099 3 2493103 NA 3.07E-08
vg0334568723 sf0334561593 3 34568723 NA 1.02E-07
vg1208075076 sf1208072482 12 8075076 NA 1.28E-07
vg1203760773 sf1203759772 12 3760773 NA 4.19E-07