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 mr1547 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
vg1003124968 sf1003123945 10 3124968 4.07E-25 1.77E-21
vg1003436810 sf1003435787 10 3436810 6.07E-22 3.62E-22
vg1003491099 sf1003490076 10 3491099 1.43E-19 1.66E-19
vg1003395810 sf1003394787 10 3395810 2.01E-15 6.00E-23
vg1215306171 sf1215303469 12 15306171 2.82E-15 1.29E-10
vg0717726887 sf0717725894 7 17726887 4.82E-13 1.36E-09
vg1003131226 sf1003130203 10 3131226 5.16E-13 3.18E-17
vg1209942861 sf1209940271 12 9942861 8.51E-13 2.06E-08
vg1003462033 sf1003461010 10 3462033 8.71E-13 4.59E-11
vg0422509978 sf0422324865 4 22509978 2.15E-12 7.76E-11
vg1003073690 sf1003072667 10 3073690 5.12E-12 4.86E-12
vg0717601450 sf0717600457 7 17601450 2.81E-10 2.45E-11
vg1003113863 sf1003112840 10 3113863 4.04E-10 2.38E-10
vg1005421909 sf1005438446 10 5421909 3.73E-08 1.86E-06
vg0709339725 sf0709338731 7 9339725 1.30E-07 6.76E-08
vg1003510976 sf1003509953 10 3510976 2.46E-07 1.81E-06
vg0623387556 sf0623386559 6 23387556 7.97E-07 3.77E-07
vg1003460005 sf1003458982 10 3460005 9.54E-07 7.32E-07
vg1127963589 sf1127491975 11 27963589 1.83E-06 1.28E-06
vg0706528880 sf0706527885 7 6528880 3.90E-06 2.41E-06
vg1016765185 sf1016693958 10 16765185 6.60E-06 2.09E-07
vg0810747174 sf0810746179 8 10747174 NA 1.42E-06
vg0611197637 sf0611196638 6 11197637 NA 2.14E-06