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 mr1038 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
vg0906091731 sf0906090731 9 6091731 6.08E-14 1.69E-09
vg0819130178 sf0819127465 8 19130178 3.06E-11 3.20E-10
vg0906217253 sf0906216253 9 6217253 3.40E-11 8.52E-08
vg0117419683 sf0117418637 1 17419683 9.63E-11 2.46E-08
vg0819055371 sf0819052658 8 19055371 1.07E-10 2.09E-12
vg0102330722 sf0102329722 1 2330722 1.45E-10 1.41E-11
vg0708154795 sf0708153800 7 8154795 2.81E-10 3.24E-09
vg0426817741 sf0426632617 4 26817741 7.76E-10 2.65E-10
vg0120297000 sf0120295955 1 20297000 3.03E-09 5.02E-08
vg0906640167 sf0906639167 9 6640167 4.76E-09 2.05E-07
vg0729253239 sf0729252247 7 29253239 5.76E-09 8.33E-09
vg0114358681 sf0114357655 1 14358681 3.34E-08 3.19E-08
vg0807538911 sf0807537916 8 7538911 3.70E-08 9.92E-09
vg1107417956 sf1107413701 11 7417956 1.10E-07 3.99E-10
vg0901039207 sf0901038207 9 1039207 1.12E-07 1.14E-08
vg0708450949 sf0708449954 7 8450949 1.66E-07 3.00E-08
vg0909848514 sf0909847513 9 9848514 2.37E-07 3.32E-08
vg1125635728 sf1125169567 11 25635728 2.59E-07 2.47E-07
vg1125932233 sf1125460647 11 25932233 4.79E-07 1.35E-07
vg0106829192 sf0106828192 1 6829192 2.43E-06 2.25E-06
vg1225034350 sf1225000803 12 25034350 NA 9.49E-09
vg0903870635 sf0903869635 9 3870635 NA 3.94E-08
vg1223629773 sf1223596229 12 23629773 NA 9.49E-08
vg0517768647 sf0517708133 5 17768647 NA 2.49E-07