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 mr1847 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
vg0817557507 sf0817554793 8 17557507 3.15E-08 3.14E-08
vg1215307750 sf1215305048 12 15307750 3.48E-08 3.48E-08
vg0805992743 sf0805991746 8 5992743 1.11E-07 1.11E-07
vg0223525077 sf0223519208 2 23525077 1.25E-07 1.25E-07
vg1020531763 sf1020460242 10 20531763 1.45E-07 1.45E-07
vg0220342715 sf0220336847 2 20342715 2.17E-07 2.17E-07
vg0420718113 sf0420546156 4 20718113 3.08E-07 3.07E-07
vg0217104494 sf0217098624 2 17104494 4.88E-07 4.88E-07
vg0726559146 sf0726558152 7 26559146 5.60E-07 5.61E-07
vg0102103204 sf0102102204 1 2103204 6.82E-07 6.82E-07
vg0516508609 sf0516451091 5 16508609 7.56E-07 7.54E-07
vg0817688257 sf0817685544 8 17688257 8.42E-07 8.43E-07
vg1209946884 sf1209944294 12 9946884 1.02E-06 1.02E-06
vg0607659813 sf0607658814 6 7659813 1.35E-06 1.34E-06
vg0630374083 sf0630373085 6 30374083 1.81E-06 1.81E-06
vg0325188819 sf0325186900 3 25188819 1.84E-06 1.83E-06
vg0801697883 sf0801696886 8 1697883 2.12E-06 2.12E-06
vg0904146189 sf0904145189 9 4146189 2.42E-06 2.42E-06
vg0808428148 sf0808427152 8 8428148 2.63E-06 2.63E-06
vg0611156063 sf0611155064 6 11156063 2.83E-06 2.82E-06