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 mr1971 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 4.29E-25 4.31E-06
vg0615093098 sf0615092099 6 15093098 2.60E-24 NA
vg0619488645 sf0619487648 6 19488645 1.73E-23 NA
vg0614107939 sf0614106940 6 14107939 3.26E-23 2.24E-07
vg0501558973 sf0501558957 5 1558973 6.57E-23 NA
vg0620812986 sf0620811989 6 20812986 7.75E-23 3.97E-07
vg0419441331 sf0419269368 4 19441331 1.33E-22 NA
vg0616858885 sf0616857887 6 16858885 1.49E-22 2.76E-06
vg0610873780 sf0610872781 6 10873780 9.61E-22 2.52E-06
vg0608916603 sf0608915604 6 8916603 NA 8.05E-09
vg1004618983 sf1004635521 10 4618983 NA 5.91E-08
vg0225867144 sf0225861275 2 25867144 NA 1.12E-07
vg0709806584 sf0709805590 7 9806584 NA 3.95E-07
vg0610802657 sf0610801658 6 10802657 NA 8.55E-07
vg1004572201 sf1004588739 10 4572201 NA 1.89E-06
vg0612638166 sf0612637167 6 12638166 NA 2.17E-06
vg1124099257 sf1123633127 11 24099257 NA 4.67E-06