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
vg0719090536 sf0719089543 7 19090536 7.43E-65 4.42E-32
vg0719064221 sf0719063228 7 19064221 1.71E-58 1.15E-34
vg0708747195 sf0708746200 7 8747195 1.24E-39 NA
vg0705563855 sf0705562856 7 5563855 4.28E-39 NA
vg0917781079 sf0917780078 9 17781079 4.23E-38 NA
vg0305273083 sf0305272083 3 5273083 4.33E-38 NA
vg0718924002 sf0718923009 7 18924002 1.38E-36 NA
vg0719091461 sf0719090468 7 19091461 NA 1.97E-24
vg0719055344 sf0719054351 7 19055344 NA 4.41E-22
vg0719192174 sf0719191181 7 19192174 NA 7.43E-16
vg0719065396 sf0719064403 7 19065396 NA 2.01E-14
vg0719316841 sf0719315848 7 19316841 NA 1.14E-09
vg0718922665 sf0718921672 7 18922665 NA 6.74E-09
vg0418071652 sf0417899693 4 18071652 NA 8.38E-09
vg0719436399 sf0719435406 7 19436399 NA 3.23E-08
vg0719466615 sf0719465622 7 19466615 NA 4.24E-08
vg1100689040 sf1100688043 11 689040 NA 4.72E-08
vg0719347879 sf0719346886 7 19347879 NA 7.11E-08
vg0620623481 sf0620622484 6 20623481 NA 1.27E-07
vg0901040131 sf0901039131 9 1040131 NA 1.45E-07
vg0719618102 sf0719617109 7 19618102 NA 1.50E-07
vg0421592157 sf0421420207 4 21592157 NA 1.87E-07
vg1105544417 sf1105540169 11 5544417 NA 3.29E-07
vg0828401472 sf0828398758 8 28401472 NA 3.39E-07
vg0329561125 sf0329554165 3 29561125 NA 3.45E-07
vg0625216580 sf0625215583 6 25216580 NA 3.72E-07
vg1018182214 sf1018110773 10 18182214 NA 7.86E-07
vg0125130007 sf0125128963 1 25130007 NA 8.76E-07
vg0517797635 sf0517737121 5 17797635 NA 1.67E-06
vg0708134630 sf0708133635 7 8134630 NA 2.32E-06
vg1217493720 sf1217487675 12 17493720 NA 2.79E-06