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 mr1478 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
vg0610871475 sf0610870476 6 10871475 1.10E-20 8.19E-10
vg0610861074 sf0610860075 6 10861074 2.16E-19 7.64E-10
vg0205541527 sf0205541527 2 5541527 1.33E-18 NA
vg0525881431 sf0525818852 5 25881431 1.72E-17 NA
vg1100320952 sf1100319954 11 320952 3.44E-17 NA
vg0615048049 sf0615047050 6 15048049 3.76E-17 NA
vg0615551230 sf0615550232 6 15551230 6.05E-15 NA
vg1222416857 sf1222383296 12 22416857 1.63E-14 NA
vg0620812986 sf0620811989 6 20812986 3.19E-14 1.28E-06
vg0502125341 sf0502125315 5 2125341 7.80E-14 2.96E-09
vg0518363321 sf0518302807 5 18363321 NA 4.12E-07
vg0614122855 sf0614121856 6 14122855 NA 8.87E-07
vg1004623296 sf1004639834 10 4623296 NA 9.75E-07
vg0608916603 sf0608915604 6 8916603 NA 1.10E-06
vg0727995401 sf0727994408 7 27995401 NA 1.28E-06
vg1004568048 sf1004584586 10 4568048 NA 1.94E-06
vg1101962356 sf1101961356 11 1962356 NA 2.41E-06
vg0140117209 sf0140116166 1 40117209 NA 2.94E-06
vg0419746635 sf0419574670 4 19746635 NA 4.36E-06
vg0906313973 sf0906312973 9 6313973 NA 4.47E-06