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 mr1104 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
vg0719007567 sf0719006574 7 19007567 5.10E-29 4.52E-18
vg0719090536 sf0719089543 7 19090536 4.07E-26 2.16E-21
vg0719133785 sf0719132792 7 19133785 2.56E-24 3.60E-16
vg0719136412 sf0719135419 7 19136412 2.12E-18 8.87E-11
vg0719195004 sf0719194011 7 19195004 1.96E-17 1.07E-10
vg1201654412 sf1201653412 12 1654412 1.38E-15 2.04E-07
vg1201345845 sf1201344845 12 1345845 1.67E-13 4.63E-08
vg0718862824 sf0718861831 7 18862824 2.13E-13 8.81E-09
vg0718998483 sf0718997490 7 18998483 NA 1.74E-11
vg0718985954 sf0718984961 7 18985954 NA 2.04E-10
vg0718885472 sf0718884479 7 18885472 NA 6.94E-09
vg0720408008 sf0720407015 7 20408008 NA 9.91E-07
vg0719450935 sf0719449942 7 19450935 NA 1.07E-06
vg0304931155 sf0304930157 3 4931155 NA 1.14E-06
vg0613011483 sf0613010484 6 13011483 NA 1.30E-06
vg0817489343 sf0817486629 8 17489343 NA 2.27E-06
vg0719140875 sf0719139882 7 19140875 NA 2.90E-06