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 mr1526 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
vg0610566084 sf0610565085 6 10566084 1.88E-46 6.13E-33
vg0610573055 sf0610572056 6 10573055 4.00E-46 5.18E-34
vg0610684942 sf0610683943 6 10684942 5.50E-42 1.24E-27
vg0610645430 sf0610644431 6 10645430 1.67E-26 1.45E-20
vg0610474412 sf0610473413 6 10474412 6.16E-26 6.07E-19
vg0610573005 sf0610572006 6 10573005 3.37E-25 3.29E-17
vg0610418414 sf0610417415 6 10418414 3.44E-25 3.63E-15
vg0610447618 sf0610446619 6 10447618 5.87E-23 1.06E-16
vg0610834756 sf0610833757 6 10834756 2.23E-22 2.99E-16
vg0610609111 sf0610608112 6 10609111 2.44E-22 3.53E-15
vg0610435285 sf0610434286 6 10435285 1.27E-21 4.49E-19
vg0610681190 sf0610680191 6 10681190 1.95E-21 1.01E-19
vg0610556004 sf0610555005 6 10556004 9.39E-19 7.83E-18
vg0610071156 sf0610070157 6 10071156 1.66E-18 1.15E-11
vg0611292337 sf0611291338 6 11292337 1.97E-16 4.28E-12
vg0611510915 sf0611509916 6 11510915 3.52E-15 9.82E-09
vg0610493119 sf0610492120 6 10493119 2.24E-14 4.16E-08
vg0610674214 sf0610673215 6 10674214 1.18E-13 2.13E-12
vg0614110509 sf0614109510 6 14110509 6.60E-13 5.47E-08
vg0611098102 sf0611097103 6 11098102 1.03E-11 2.06E-09
vg0610211069 sf0610210070 6 10211069 1.03E-10 8.59E-09
vg0611654043 sf0611653044 6 11654043 1.42E-10 6.05E-09
vg0611628409 sf0611627410 6 11628409 4.53E-10 7.35E-10
vg0613809145 sf0613808146 6 13809145 7.90E-10 5.60E-08
vg0610449310 sf0610448311 6 10449310 1.17E-09 4.75E-08
vg0611636429 sf0611635430 6 11636429 5.09E-08 3.41E-09
vg0610127588 sf0610126589 6 10127588 NA 5.19E-12