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 mr1188 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
vg0142372020 sf0142370976 1 42372020 3.55E-18 NA
vg0222625642 sf0222619773 2 22625642 7.96E-16 5.91E-06
vg1108796428 sf1108791038 11 8796428 1.11E-15 5.92E-06
vg0222036258 sf0222030389 2 22036258 1.10E-14 NA
vg1108491572 sf1108486182 11 8491572 1.48E-14 2.65E-06
vg0320137682 sf0320136193 3 20137682 1.89E-14 NA
vg0906561460 sf0906560460 9 6561460 3.08E-14 8.13E-06
vg0222574285 sf0222568416 2 22574285 2.75E-13 1.47E-06
vg0319088905 sf0319087665 3 19088905 6.98E-13 NA
vg0319082948 sf0319081708 3 19082948 8.81E-13 2.60E-06
vg0235186964 sf0235181095 2 35186964 1.58E-12 2.68E-06
vg0235271789 sf0235265920 2 35271789 2.75E-12 1.76E-06
vg0630551197 sf0630550199 6 30551197 NA 2.02E-07
vg0630338357 sf0630337359 6 30338357 NA 6.87E-07
vg0821456788 sf0821454075 8 21456788 NA 7.44E-07
vg0311912847 sf0311911565 3 11912847 NA 7.71E-07
vg0629150340 sf0629149342 6 29150340 NA 9.03E-07
vg0523780082 sf0523717503 5 23780082 NA 9.13E-07
vg1114018010 sf1113554331 11 14018010 NA 9.16E-07
vg0205435877 sf0205435877 2 5435877 NA 1.37E-06
vg1108876734 sf1108871344 11 8876734 NA 1.87E-06
vg0720001039 sf0720000046 7 20001039 NA 2.60E-06
vg0717539471 sf0717538478 7 17539471 NA 3.17E-06
vg1114456299 sf1113992616 11 14456299 NA 3.30E-06