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 mr1245 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
vg1103155824 sf1103151727 11 3155824 4.98E-08 8.33E-07
vg0819985304 sf0819982591 8 19985304 8.73E-08 9.51E-07
vg0717125729 sf0717124736 7 17125729 4.95E-07 1.88E-07
vg0420718113 sf0420546156 4 20718113 5.19E-07 1.04E-06
vg1000501145 sf1000500121 10 501145 6.45E-07 2.41E-07
vg0325188819 sf0325186900 3 25188819 9.60E-07 2.29E-06
vg0232208358 sf0232202489 2 32208358 1.26E-06 2.69E-06
vg0516302066 sf0516244548 5 16302066 1.78E-06 2.83E-06
vg0714748935 sf0714747942 7 14748935 1.88E-06 1.19E-06
vg0521872068 sf0521809510 5 21872068 2.88E-06 1.60E-06
vg1215307750 sf1215305048 12 15307750 3.10E-06 2.01E-06
vg0710251892 sf0710250898 7 10251892 3.14E-06 1.87E-06
vg0420503850 sf0420331894 4 20503850 4.02E-06 3.64E-06
vg0105393860 sf0105392860 1 5393860 6.15E-06 1.10E-06
vg1000702985 sf1000701961 10 702985 7.04E-06 1.66E-06
vg0715403959 sf0715402966 7 15403959 NA 9.03E-07
vg0421318693 sf0421146747 4 21318693 NA 2.50E-06
vg0221240541 sf0221234673 2 21240541 NA 3.18E-06
vg0305903582 sf0305902582 3 5903582 NA 3.34E-06
vg0623014541 sf0623013544 6 23014541 NA 3.55E-06
vg0510460804 sf0510460733 5 10460804 NA 3.98E-06
vg0235607025 sf0235601156 2 35607025 NA 8.43E-06