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 mr1181 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
vg0724504161 sf0724503167 7 24504161 2.23E-11 2.23E-11
vg0517732975 sf0517672616 5 17732975 4.86E-07 4.86E-07
vg0717886286 sf0717885293 7 17886286 5.70E-07 5.70E-07
vg1016294522 sf1016223298 10 16294522 8.03E-07 8.03E-07
vg1107663436 sf1107659181 11 7663436 8.06E-07 8.07E-07
vg0309318200 sf0309317136 3 9318200 8.87E-07 8.87E-07
vg0517768858 sf0517708344 5 17768858 9.01E-07 9.01E-07
vg0624461841 sf0624460844 6 24461841 9.08E-07 9.08E-07
vg0800993769 sf0800992771 8 993769 9.67E-07 9.67E-07
vg0607490138 sf0607489139 6 7490138 2.23E-06 2.23E-06
vg0141988740 sf0141987697 1 41988740 2.67E-06 2.67E-06
vg0603214907 sf0603213908 6 3214907 3.07E-06 3.07E-06
vg0223215105 sf0223209236 2 23215105 3.70E-06 3.70E-06
vg0117632054 sf0117631008 1 17632054 3.74E-06 3.74E-06
vg1122418019 sf1121951890 11 22418019 4.12E-06 4.12E-06
vg1120893049 sf1120426952 11 20893049 4.23E-06 4.23E-06
vg0133657125 sf0133656081 1 33657125 6.81E-06 6.81E-06