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 mr1260 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
vg0423906532 sf0423721392 4 23906532 1.63E-08 1.63E-08
vg1121219893 sf1120753771 11 21219893 1.41E-07 1.41E-07
vg1121220731 sf1120754609 11 21220731 1.94E-07 1.94E-07
vg1000239938 sf1000238938 10 239938 3.46E-07 3.46E-07
vg0913674199 sf0913673198 9 13674199 3.67E-07 3.67E-07
vg0706405260 sf0706404265 7 6405260 4.16E-07 4.16E-07
vg0125636241 sf0125635197 1 25636241 5.24E-07 5.24E-07
vg0909866383 sf0909865382 9 9866383 5.40E-07 5.40E-07
vg0610394032 sf0610393033 6 10394032 9.89E-07 9.89E-07
vg0705161092 sf0705160093 7 5161092 1.10E-06 1.10E-06
vg0727791557 sf0727790564 7 27791557 1.14E-06 1.14E-06
vg0425422291 sf0425237151 4 25422291 1.47E-06 1.47E-06
vg0210599887 sf0210599885 2 10599887 1.62E-06 1.62E-06
vg1016928784 sf1016857556 10 16928784 2.58E-06 2.58E-06
vg1009652409 sf1009581230 10 9652409 3.04E-06 3.04E-06
vg0309808587 sf0309807523 3 9808587 3.20E-06 3.20E-06
vg0606682474 sf0606681475 6 6682474 3.25E-06 3.25E-06
vg1121991352 sf1121525223 11 21991352 3.37E-06 3.37E-06
vg0515438605 sf0515381146 5 15438605 3.70E-06 3.70E-06
vg0714860097 sf0714859104 7 14860097 4.25E-06 4.25E-06
vg1107588911 sf1107584656 11 7588911 4.83E-06 4.83E-06
vg0121389895 sf0121388850 1 21389895 7.90E-06 7.90E-06