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 mr1114 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
vg1008520987 sf1008449849 10 8520987 9.05E-15 1.92E-11
vg0407823910 sf0407819178 4 7823910 2.33E-12 3.22E-07
vg0407825687 sf0407820955 4 7825687 5.02E-12 1.07E-08
vg1005827029 sf1005843567 10 5827029 2.33E-11 3.28E-08
vg1005827020 sf1005843558 10 5827020 3.11E-11 3.01E-08
vg1216843191 sf1216837145 12 16843191 9.74E-11 2.36E-07
vg1005441451 sf1005457988 10 5441451 1.55E-10 9.95E-06
vg1216843502 sf1216837456 12 16843502 3.36E-10 1.25E-07
vg0716828374 sf0716827381 7 16828374 9.51E-10 3.07E-06
vg1007140460 sf1007156083 10 7140460 1.20E-09 3.24E-08
vg0501793703 sf0501793686 5 1793703 7.37E-09 4.14E-06
vg0905577010 sf0905576010 9 5577010 1.64E-08 3.16E-06
vg0220796750 sf0220790882 2 20796750 1.83E-08 4.14E-06
vg0412853605 sf0412844314 4 12853605 4.82E-08 4.54E-06
vg0220790529 sf0220784661 2 20790529 6.14E-08 7.11E-06
vg0714931175 sf0714930182 7 14931175 5.42E-07 8.04E-07
vg0331997832 sf0331990709 3 31997832 1.02E-06 2.10E-06
vg0610056324 sf0610055325 6 10056324 1.18E-06 NA
vg0335792519 sf0335785388 3 35792519 2.04E-06 1.89E-06
vg0803452485 sf0803451488 8 3452485 5.67E-06 NA
vg0720056770 sf0720055777 7 20056770 9.18E-06 NA
vg0118425804 sf0118424758 1 18425804 9.61E-06 NA
vg0618501224 sf0618500227 6 18501224 NA 1.29E-06
vg1216729892 sf1216723846 12 16729892 NA 5.56E-06