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 mr1750 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
vg1216994127 sf1216988081 12 16994127 2.98E-10 2.98E-10
vg1209876216 sf1209873626 12 9876216 5.42E-10 5.42E-10
vg1220059260 sf1220030702 12 20059260 9.09E-09 9.09E-09
vg1123222536 sf1122756407 11 23222536 2.31E-08 2.31E-08
vg0710881106 sf0710880112 7 10881106 3.37E-08 3.37E-08
vg0600569739 sf0600568740 6 569739 5.17E-08 5.17E-08
vg0818417541 sf0818414828 8 18417541 6.50E-08 6.50E-08
vg0231411574 sf0231405705 2 31411574 6.21E-07 6.21E-07
vg1219821279 sf1219792749 12 19821279 7.29E-07 7.29E-07
vg0139276484 sf0139275441 1 39276484 9.98E-07 9.98E-07
vg0311072594 sf0311071312 3 11072594 1.17E-06 1.17E-06
vg1218863509 sf1218834944 12 18863509 1.34E-06 1.34E-06
vg0314138520 sf0314137209 3 14138520 1.59E-06 1.59E-06
vg0712130165 sf0712129171 7 12130165 1.66E-06 1.66E-06
vg1215551588 sf1215548885 12 15551588 1.68E-06 1.68E-06
vg0916734760 sf0916733759 9 16734760 1.78E-06 1.78E-06
vg0921387658 sf0921387177 9 21387658 1.78E-06 1.78E-06
vg1223731338 sf1223697791 12 23731338 1.82E-06 1.82E-06
vg0605114474 sf0605113475 6 5114474 2.14E-06 2.14E-06
vg0817059251 sf0817056537 8 17059251 2.26E-06 2.26E-06