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 mr1453 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
vg0919141927 sf0919141516 9 19141927 1.70E-08 1.70E-08
vg0709448532 sf0709447538 7 9448532 3.51E-07 3.51E-07
vg0716252058 sf0716251065 7 16252058 4.38E-07 4.38E-07
vg0716279747 sf0716278754 7 16279747 7.58E-07 7.58E-07
vg1023172834 sf1023101306 10 23172834 1.49E-06 1.49E-06
vg0715036888 sf0715035895 7 15036888 1.59E-06 1.59E-06
vg0312184618 sf0312183336 3 12184618 1.87E-06 1.87E-06
vg0202968896 sf0202968894 2 2968896 1.98E-06 1.98E-06
vg0727110534 sf0727109540 7 27110534 2.21E-06 2.21E-06
vg0603303648 sf0603302649 6 3303648 2.31E-06 2.31E-06
vg1114618741 sf1114155059 11 14618741 2.58E-06 2.58E-06
vg0130239724 sf0130238679 1 30239724 3.31E-06 3.31E-06
vg0713895671 sf0713894678 7 13895671 3.32E-06 3.32E-06
vg0516508609 sf0516451091 5 16508609 4.51E-06 4.51E-06