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 mr1197 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
vg0805973370 sf0805972373 8 5973370 2.17E-08 2.17E-08
vg0222578508 sf0222572639 2 22578508 1.42E-07 1.42E-07
vg0114130447 sf0114129421 1 14130447 3.45E-07 3.45E-07
vg0619163386 sf0619162389 6 19163386 4.00E-07 4.00E-07
vg1224211269 sf1224177722 12 24211269 6.56E-07 6.56E-07
vg0622365879 sf0622364882 6 22365879 7.02E-07 7.02E-07
vg0505178248 sf0505178226 5 5178248 7.63E-07 7.64E-07
vg0611950802 sf0611949803 6 11950802 8.70E-07 8.70E-07
vg0221699975 sf0221694106 2 21699975 1.25E-06 1.25E-06
vg0113920566 sf0113919540 1 13920566 1.46E-06 1.46E-06
vg0221185352 sf0221179484 2 21185352 1.47E-06 1.47E-06
vg0811697470 sf0811696475 8 11697470 1.65E-06 1.65E-06
vg1000903085 sf1000902061 10 903085 1.84E-06 1.84E-06
vg0110736403 sf0110735379 1 10736403 2.15E-06 2.15E-06
vg1120290807 sf1119824731 11 20290807 2.46E-06 2.46E-06
vg1003471515 sf1003470492 10 3471515 2.73E-06 2.73E-06
vg1112948764 sf1112485085 11 12948764 2.95E-06 2.95E-06
vg1105189380 sf1105185191 11 5189380 4.09E-06 4.09E-06
vg0611924884 sf0611923885 6 11924884 4.10E-06 4.10E-06
vg0326972463 sf0326965516 3 26972463 4.12E-06 4.12E-06