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 mr1919 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
vg0226834402 sf0226828533 2 26834402 3.43E-09 3.44E-09
vg0809143046 sf0809142050 8 9143046 1.81E-08 1.81E-08
vg0415538057 sf0415528744 4 15538057 4.54E-08 4.56E-08
vg0805435614 sf0805434617 8 5435614 1.97E-07 1.97E-07
vg0329205463 sf0329198515 3 29205463 4.76E-07 4.77E-07
vg0703531849 sf0703530850 7 3531849 4.82E-07 4.84E-07
vg0103530099 sf0103529099 1 3530099 4.83E-07 4.84E-07
vg0813870236 sf0813867522 8 13870236 6.84E-07 6.87E-07
vg0528560614 sf0528497969 5 28560614 1.05E-06 1.05E-06
vg0525819539 sf0525756960 5 25819539 1.44E-06 1.45E-06
vg0813117473 sf0813115033 8 13117473 1.54E-06 1.54E-06
vg0127890553 sf0127889509 1 27890553 1.85E-06 1.86E-06
vg0503062538 sf0503062514 5 3062538 2.27E-06 2.28E-06
vg0520975375 sf0520912816 5 20975375 2.33E-06 2.34E-06
vg0527948989 sf0527886345 5 27948989 2.37E-06 2.38E-06
vg0203685324 sf0203685321 2 3685324 3.18E-06 3.20E-06
vg0224523120 sf0224517251 2 24523120 3.18E-06 3.17E-06
vg1015373114 sf1015301882 10 15373114 3.50E-06 3.52E-06
vg0403210904 sf0403206507 4 3210904 3.88E-06 3.89E-06
vg0141839410 sf0141838367 1 41839410 3.99E-06 4.00E-06