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 mr1424 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
vg1213717956 sf1213715294 12 13717956 2.07E-08 2.07E-08
vg1102677343 sf1102673247 11 2677343 2.31E-08 2.32E-08
vg0921699962 sf0921699481 9 21699962 3.25E-08 3.25E-08
vg0329810087 sf0329803126 3 29810087 5.55E-08 5.55E-08
vg1215482015 sf1215479312 12 15482015 1.52E-07 1.52E-07
vg0706126992 sf0706125993 7 6126992 1.68E-07 1.68E-07
vg1204324619 sf1204323607 12 4324619 2.45E-07 2.45E-07
vg0217857667 sf0217851798 2 17857667 3.65E-07 3.66E-07
vg1220914154 sf1220880703 12 20914154 4.88E-07 4.88E-07
vg0812614441 sf0812612266 8 12614441 5.91E-07 5.91E-07
vg0125628571 sf0125627527 1 25628571 8.52E-07 8.53E-07
vg0918918596 sf0918917596 9 18918596 8.96E-07 8.96E-07
vg0609213350 sf0609212351 6 9213350 9.77E-07 9.77E-07
vg1215077450 sf1215074791 12 15077450 1.01E-06 1.01E-06
vg1002006293 sf1002005270 10 2006293 1.03E-06 1.03E-06
vg0313058915 sf0313057633 3 13058915 1.64E-06 1.64E-06
vg0403315819 sf0403311422 4 3315819 1.99E-06 1.99E-06
vg0815562300 sf0815559586 8 15562300 2.21E-06 2.21E-06
vg0223262220 sf0223256351 2 23262220 2.21E-06 2.21E-06
vg1004886820 sf1004903357 10 4886820 2.28E-06 2.28E-06