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 mr1499 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
vg0232486002 sf0232480133 2 32486002 1.39E-08 1.39E-08
vg0906975807 sf0906974807 9 6975807 1.58E-08 1.58E-08
vg1012832874 sf1012761689 10 12832874 3.23E-08 3.23E-08
vg0202919618 sf0202919616 2 2919618 4.21E-08 4.21E-08
vg0511176472 sf0511176401 5 11176472 4.77E-08 4.77E-08
vg0720609830 sf0720608837 7 20609830 6.38E-08 6.38E-08
vg0331560335 sf0331553212 3 31560335 2.10E-07 2.10E-07
vg0226331103 sf0226325234 2 26331103 2.20E-07 2.20E-07
vg0627876339 sf0627875341 6 27876339 2.86E-07 2.85E-07
vg0220752536 sf0220746668 2 20752536 4.03E-07 4.03E-07
vg0434586605 sf0434401497 4 34586605 4.34E-07 4.34E-07
vg0500807732 sf0500807714 5 807732 4.44E-07 4.44E-07
vg1013614980 sf1013543750 10 13614980 7.46E-07 7.46E-07
vg0400952352 sf0400947904 4 952352 8.32E-07 8.32E-07
vg0101141375 sf0101140375 1 1141375 1.21E-06 1.21E-06
vg0135156282 sf0135155239 1 35156282 1.29E-06 1.29E-06
vg0232799246 sf0232793377 2 32799246 1.37E-06 1.37E-06
vg1004234880 sf1004251418 10 4234880 1.61E-06 1.61E-06
vg0910456701 sf0910455700 9 10456701 1.62E-06 1.62E-06
vg1102888595 sf1102884499 11 2888595 1.77E-06 1.77E-06