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 mr1389 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
vg0728442720 sf0728441728 7 28442720 4.43E-30 2.30E-17
vg1222591917 sf1222558356 12 22591917 8.79E-25 4.35E-16
vg0728693760 sf0728692768 7 28693760 3.38E-23 1.73E-17
vg0328157393 sf0328150447 3 28157393 8.03E-23 1.36E-07
vg0330661173 sf0330654060 3 30661173 2.69E-22 6.16E-07
vg0631155509 sf0631154511 6 31155509 1.31E-21 4.63E-09
vg0417792314 sf0417620352 4 17792314 1.28E-18 3.23E-11
vg0728490926 sf0728489934 7 28490926 8.51E-18 5.10E-13
vg0219834070 sf0219828202 2 19834070 1.21E-17 9.74E-11
vg0319440543 sf0319439054 3 19440543 7.61E-17 1.94E-09
vg0325722534 sf0325720552 3 25722534 1.31E-16 1.06E-11
vg0616470948 sf0616469950 6 16470948 1.88E-16 3.24E-10
vg0526329290 sf0526266653 5 26329290 9.79E-15 2.64E-08
vg1219449222 sf1219420692 12 19449222 1.10E-14 1.31E-10
vg1206967731 sf1206966621 12 6967731 5.12E-13 3.30E-09
vg1223502712 sf1223469172 12 23502712 1.72E-12 9.54E-11
vg0630964914 sf0630963916 6 30964914 2.00E-12 2.30E-07
vg0728951005 sf0728950013 7 28951005 9.67E-12 9.11E-09
vg0312369772 sf0312368490 3 12369772 1.34E-10 1.67E-08
vg0140074301 sf0140073258 1 40074301 4.20E-10 7.76E-09
vg0713786254 sf0713785261 7 13786254 2.19E-08 3.62E-09
vg0304762695 sf0304761697 3 4762695 2.85E-08 3.04E-10
vg1222877206 sf1222843646 12 22877206 4.27E-08 2.93E-08
vg0100792291 sf0100791291 1 792291 9.26E-07 NA
vg1222465137 sf1222431576 12 22465137 NA 2.10E-08
vg1225139875 sf1225106329 12 25139875 NA 4.29E-07
vg1119756834 sf1119290522 11 19756834 NA 1.49E-06