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 mr1653 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
vg1020183524 sf1020112022 10 20183524 4.54E-11 NA
vg1214674547 sf1214671886 12 14674547 7.44E-11 1.60E-06
vg0706209943 sf0706208944 7 6209943 1.52E-10 3.55E-07
vg1214823650 sf1214820991 12 14823650 4.14E-10 3.56E-08
vg0421025376 sf0420853429 4 21025376 4.30E-10 4.10E-06
vg0223262220 sf0223256351 2 23262220 4.32E-10 1.82E-07
vg0706170362 sf0706169363 7 6170362 1.01E-09 1.45E-06
vg0227802642 sf0227796773 2 27802642 1.18E-09 1.95E-06
vg0608860852 sf0608859853 6 8860852 5.15E-09 1.65E-06
vg1006743978 sf1006759601 10 6743978 9.06E-09 2.23E-06
vg0207729665 sf0207729664 2 7729665 1.31E-08 1.91E-07
vg0312773945 sf0312772663 3 12773945 1.54E-08 1.42E-06
vg0908229421 sf0908228421 9 8229421 3.18E-08 2.00E-06