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 mr1040 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
vg0817612440 sf0817609727 8 17612440 1.41E-22 8.66E-10
vg0817615040 sf0817612327 8 17615040 1.27E-21 2.02E-10
vg0812793667 sf0812791492 8 12793667 9.61E-20 1.55E-06
vg0115669420 sf0115668394 1 15669420 2.01E-19 NA
vg0432701215 sf0432516104 4 32701215 1.87E-18 1.38E-06
vg0628353577 sf0628352579 6 28353577 1.97E-18 NA
vg1205231991 sf1205230977 12 5231991 8.03E-18 NA
vg0608184995 sf0608183996 6 8184995 9.27E-17 NA
vg0433044174 sf0432859061 4 33044174 3.06E-16 NA
vg0817558529 sf0817555815 8 17558529 NA 2.85E-08
vg0817608700 sf0817605987 8 17608700 NA 2.45E-07
vg0601639995 sf0601638996 6 1639995 NA 3.70E-07
vg1214656787 sf1214654127 12 14656787 NA 5.84E-07
vg0818128211 sf0818125498 8 18128211 NA 6.87E-07
vg1214965191 sf1214962533 12 14965191 NA 8.10E-07
vg0810682226 sf0810681230 8 10682226 NA 2.22E-06
vg0815549377 sf0815546663 8 15549377 NA 3.65E-06
vg1208634025 sf1208631432 12 8634025 NA 3.76E-06
vg0413426647 sf0413417361 4 13426647 NA 3.93E-06