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 mr1758 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
vg1116008747 sf1115543619 11 16008747 2.02E-117 1.03E-14
vg1116239941 sf1115774811 11 16239941 1.19E-116 3.01E-15
vg1111472931 sf1111467248 11 11472931 5.55E-116 5.18E-14
vg0304846806 sf0304845808 3 4846806 3.96E-103 6.41E-06
vg0903435730 sf0903434730 9 3435730 1.07E-99 NA
vg0802078087 sf0802077090 8 2078087 3.37E-96 NA
vg0714630012 sf0714629019 7 14630012 6.11E-94 1.43E-07
vg0614107939 sf0614106940 6 14107939 2.12E-88 5.98E-08
vg0621048541 sf0621047544 6 21048541 NA 1.61E-08
vg1100988116 sf1100987117 11 988116 NA 2.99E-07
vg0717311702 sf0717310709 7 17311702 NA 3.74E-07
vg1111075762 sf1111070079 11 11075762 NA 4.13E-07
vg1005203236 sf1005219773 10 5203236 NA 9.30E-07
vg0129918349 sf0129917304 1 29918349 NA 1.24E-06
vg0134264091 sf0134263048 1 34264091 NA 1.35E-06
vg0129917132 sf0129916087 1 29917132 NA 1.66E-06
vg0904574302 sf0904573302 9 4574302 NA 3.01E-06
vg0430673719 sf0430488594 4 30673719 NA 3.16E-06
vg1124633481 sf1124167321 11 24633481 NA 4.27E-06
vg0430702115 sf0430516990 4 30702115 NA 4.82E-06