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 mr1004 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
vg0915556027 sf0915555026 9 15556027 2.10E-10 NA
vg1105599945 sf1105595697 11 5599945 6.63E-10 NA
vg0921446168 sf0921445687 9 21446168 9.72E-10 6.64E-07
vg0603022263 sf0603021264 6 3022263 1.01E-09 NA
vg0131664724 sf0131663680 1 31664724 1.40E-09 NA
vg1224533879 sf1224500333 12 24533879 1.72E-09 4.63E-06
vg0328200064 sf0328193118 3 28200064 4.54E-09 NA
vg0921420005 sf0921419524 9 21420005 7.78E-09 3.70E-06
vg0528462620 sf0528399975 5 28462620 8.34E-09 3.54E-06
vg0525062159 sf0524999574 5 25062159 1.01E-08 4.10E-06
vg0909000770 sf0908999769 9 9000770 8.12E-08 2.48E-06
vg0211510634 sf0211510630 2 11510634 9.46E-08 2.25E-07
vg0612510076 sf0612509077 6 12510076 5.20E-07 7.73E-07
vg0215099729 sf0215093859 2 15099729 6.03E-07 9.93E-09
vg0215099748 sf0215093878 2 15099748 1.88E-06 6.49E-09
vg1117142352 sf1116676204 11 17142352 2.13E-06 NA
vg0816652216 sf0816649502 8 16652216 4.02E-06 5.17E-07
vg1216034397 sf1216031693 12 16034397 4.14E-06 9.89E-08
vg0305823661 sf0305822661 3 5823661 NA 4.97E-08
vg0910517345 sf0910516344 9 10517345 NA 3.77E-07
vg0421477325 sf0421305376 4 21477325 NA 8.89E-07
vg1224168671 sf1224135125 12 24168671 NA 1.27E-06
vg1214358313 sf1214355653 12 14358313 NA 1.71E-06
vg0203269607 sf0203269605 2 3269607 NA 2.07E-06
vg0328746435 sf0328739489 3 28746435 NA 2.68E-06
vg0623502559 sf0623501562 6 23502559 NA 3.41E-06
vg0322975067 sf0322973555 3 22975067 NA 9.22E-06