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 mr1987 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
vg1219821279 sf1219792749 12 19821279 7.19E-10 7.19E-10
vg1219118839 sf1219090275 12 19118839 8.24E-09 8.24E-09
vg0105393860 sf0105392860 1 5393860 9.14E-07 9.14E-07
vg0710881106 sf0710880112 7 10881106 1.08E-06 1.08E-06
vg0700217233 sf0700216233 7 217233 1.17E-06 1.17E-06
vg1209876216 sf1209873626 12 9876216 1.36E-06 1.36E-06
vg0128471692 sf0128470647 1 28471692 1.51E-06 1.51E-06
vg0600569739 sf0600568740 6 569739 1.76E-06 1.76E-06
vg0416982091 sf0416810133 4 16982091 2.01E-06 2.01E-06
vg1215551588 sf1215548885 12 15551588 2.01E-06 2.01E-06
vg0916662225 sf0916661224 9 16662225 2.32E-06 2.32E-06
vg0108564628 sf0108563628 1 8564628 3.13E-06 3.13E-06
vg0204718286 sf0204718283 2 4718286 3.95E-06 3.95E-06
vg0509333551 sf0509333480 5 9333551 4.93E-06 4.93E-06