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 mr1613 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
vg0406995300 sf0406990571 4 6995300 2.24E-21 2.25E-14
vg0222746228 sf0222740359 2 22746228 1.59E-16 3.70E-10
vg0406944654 sf0406939922 4 6944654 3.81E-16 9.58E-10
vg0222739831 sf0222733962 2 22739831 4.39E-14 8.00E-10
vg0412100387 sf0412091098 4 12100387 1.56E-12 5.75E-09
vg0406592386 sf0406587830 4 6592386 1.68E-12 3.28E-09
vg0406620827 sf0406616271 4 6620827 4.51E-12 6.15E-06
vg0424423524 sf0424238385 4 24423524 8.90E-12 1.95E-08
vg0407872167 sf0407867435 4 7872167 1.42E-11 1.25E-11
vg1215995140 sf1215992436 12 15995140 2.14E-11 3.92E-07
vg1216282971 sf1216280267 12 16282971 7.72E-11 1.76E-08
vg1216282887 sf1216280183 12 16282887 1.09E-10 1.11E-08
vg0412144728 sf0412135439 4 12144728 8.83E-10 2.29E-08
vg0412292000 sf0412282715 4 12292000 8.89E-10 6.87E-11
vg0411431095 sf0411421797 4 11431095 1.46E-09 1.91E-09
vg0222852279 sf0222846410 2 22852279 2.97E-09 2.03E-08
vg1216930362 sf1216924316 12 16930362 3.04E-09 6.52E-08
vg1215976459 sf1215973755 12 15976459 3.48E-09 7.29E-10
vg1209644369 sf1209641778 12 9644369 4.41E-09 1.88E-08
vg0407013946 sf0407009217 4 7013946 2.42E-08 9.23E-08
vg1107318404 sf1107314149 11 7318404 4.78E-08 3.34E-08
vg0400257725 sf0400256725 4 257725 NA 1.57E-10
vg0117431722 sf0117430676 1 17431722 NA 1.36E-08
vg1005181911 sf1005198448 10 5181911 NA 2.04E-08
vg1226253312 sf1226219706 12 26253312 NA 2.59E-08