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 mr1667 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
vg1125475681 sf1125009520 11 25475681 4.84E-19 4.81E-12
vg1125475628 sf1125009467 11 25475628 3.10E-18 2.30E-12
vg0713260653 sf0713259660 7 13260653 2.17E-14 2.81E-08
vg0612546146 sf0612545147 6 12546146 1.55E-11 7.49E-07
vg1123611068 sf1123144938 11 23611068 7.93E-10 8.30E-06
vg1123627766 sf1123161636 11 23627766 2.02E-09 4.35E-06
vg0421406871 sf0421234924 4 21406871 2.23E-09 NA
vg1126224167 sf1125752581 11 26224167 1.65E-08 3.04E-06
vg1125426100 sf1124959939 11 25426100 5.06E-08 7.70E-07
vg1127787917 sf1127316303 11 27787917 7.12E-08 4.48E-07
vg0912209993 sf0912208992 9 12209993 1.85E-06 NA
vg0234519849 sf0234513980 2 34519849 7.05E-06 NA
vg0224889308 sf0224883439 2 24889308 NA 3.38E-06