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 mr1087 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
vg0610606146 sf0610605147 6 10606146 2.83E-56 1.03E-40
vg0610683007 sf0610682008 6 10683007 5.68E-51 7.52E-41
vg0610471911 sf0610470912 6 10471911 2.99E-47 3.92E-32
vg0610435111 sf0610434112 6 10435111 1.96E-34 7.69E-25
vg0610476418 sf0610475419 6 10476418 3.25E-29 5.25E-17
vg0610410785 sf0610409786 6 10410785 6.98E-28 1.05E-18
vg0610843263 sf0610842264 6 10843263 4.61E-25 1.22E-15
vg0610874933 sf0610873934 6 10874933 2.51E-24 9.42E-14
vg0610405525 sf0610404526 6 10405525 6.48E-23 3.79E-16
vg0610375991 sf0610374992 6 10375991 1.58E-20 5.03E-16
vg0610608910 sf0610607911 6 10608910 2.49E-19 1.38E-07
vg0610532353 sf0610531354 6 10532353 4.40E-18 6.79E-11
vg0610205132 sf0610204133 6 10205132 8.24E-16 6.14E-11
vg0616574004 sf0616573006 6 16574004 1.03E-15 4.88E-06
vg0617815455 sf0617814458 6 17815455 2.20E-15 3.24E-09
vg0610611540 sf0610610541 6 10611540 3.26E-15 1.27E-11
vg0611292337 sf0611291338 6 11292337 5.63E-15 5.95E-09
vg0611512029 sf0611511030 6 11512029 1.36E-13 6.69E-08
vg0611654043 sf0611653044 6 11654043 2.65E-13 1.40E-08
vg0610957761 sf0610956762 6 10957761 1.22E-11 3.92E-09
vg0610075482 sf0610074483 6 10075482 1.10E-10 3.47E-08
vg0611340585 sf0611339586 6 11340585 2.63E-10 3.25E-07
vg0610633502 sf0610632503 6 10633502 5.84E-10 1.70E-07
vg0610635812 sf0610634813 6 10635812 3.73E-09 3.93E-09
vg1116562086 sf1116096964 11 16562086 1.01E-07 5.00E-08
vg0610132636 sf0610131637 6 10132636 1.71E-07 2.26E-07
vg0404977420 sf0404972859 4 4977420 NA 1.40E-07
vg0610418246 sf0610417247 6 10418246 NA 3.21E-06