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 mr1226 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
vg0719006525 sf0719005532 7 19006525 7.63E-24 2.13E-22
vg0719079366 sf0719078373 7 19079366 6.46E-23 1.43E-21
vg0228933475 sf0228927606 2 28933475 2.28E-12 5.93E-09
vg0719135307 sf0719134314 7 19135307 2.66E-12 1.02E-17
vg0107198487 sf0107197487 1 7198487 4.30E-12 1.01E-07
vg0719040022 sf0719039029 7 19040022 2.65E-11 2.92E-18
vg0417642687 sf0417470728 4 17642687 3.28E-11 8.29E-07
vg1020494793 sf1020423272 10 20494793 3.72E-11 9.59E-09
vg0707738691 sf0707737696 7 7738691 1.63E-10 3.45E-09
vg1101911438 sf1101910439 11 1911438 4.06E-10 4.09E-11
vg0422855440 sf0422670325 4 22855440 1.11E-09 1.83E-07
vg0700923552 sf0700922552 7 923552 1.65E-09 3.95E-09
vg0432630329 sf0432445218 4 32630329 2.60E-09 1.48E-07
vg0800964801 sf0800963803 8 964801 2.88E-09 1.37E-07
vg1107392564 sf1107388309 11 7392564 4.39E-09 1.68E-07
vg0811122646 sf0811121651 8 11122646 4.64E-09 4.08E-09
vg0418074959 sf0417903000 4 18074959 5.99E-08 3.20E-08
vg0124647921 sf0124646877 1 24647921 6.45E-08 6.15E-10
vg0625303878 sf0625302881 6 25303878 1.56E-07 2.32E-07
vg0700550440 sf0700549440 7 550440 5.60E-07 1.27E-07
vg0329561125 sf0329554165 3 29561125 NA 4.13E-08
vg0312684585 sf0312683303 3 12684585 NA 5.36E-08
vg0714249785 sf0714248792 7 14249785 NA 2.25E-07