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 mr1744 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
vg0709172447 sf0709171453 7 9172447 8.88E-16 NA
vg0919888624 sf0919888143 9 19888624 2.46E-15 NA
vg0705226228 sf0705225229 7 5226228 3.05E-15 NA
vg0905464468 sf0905463468 9 5464468 4.95E-15 NA
vg0200903122 sf0200903122 2 903122 8.36E-15 NA
vg0122694221 sf0122693176 1 22694221 3.38E-13 7.61E-06
vg1003030170 sf1003029147 10 3030170 4.81E-13 NA
vg1204270078 sf1204269066 12 4270078 6.25E-12 NA