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 mr1720 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
vg1204622168 sf1204621156 12 4622168 5.52E-11 1.14E-08
vg0720805926 sf0720804933 7 20805926 3.71E-09 4.58E-09
vg0105931184 sf0105930184 1 5931184 2.09E-08 1.12E-06
vg0611626674 sf0611625675 6 11626674 4.84E-08 6.00E-06
vg0134365775 sf0134364732 1 34365775 9.00E-08 7.90E-09
vg0427914020 sf0427728883 4 27914020 3.30E-07 2.58E-06
vg1119545646 sf1119079334 11 19545646 3.40E-07 2.36E-06
vg0721581927 sf0721580934 7 21581927 4.16E-06 1.36E-06
vg0128855514 sf0128854469 1 28855514 4.87E-06 NA
vg0432747868 sf0432562754 4 32747868 5.05E-06 1.03E-06
vg0907480791 sf0907479791 9 7480791 8.30E-06 4.62E-06