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 mr1100 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
vg0406465683 sf0406461126 4 6465683 4.66E-31 9.43E-22
vg0817327521 sf0817324807 8 17327521 5.01E-14 8.02E-09
vg1004380487 sf1004397025 10 4380487 9.51E-12 7.02E-07
vg0406785791 sf0406781236 4 6785791 1.80E-10 NA
vg1004481242 sf1004497780 10 4481242 1.88E-10 5.00E-08
vg1222455166 sf1222421605 12 22455166 2.38E-10 1.97E-06
vg0406056794 sf0406052233 4 6056794 5.00E-10 1.21E-07
vg1215215031 sf1215212328 12 15215031 3.48E-09 NA
vg0823019901 sf0823017188 8 23019901 4.46E-09 1.74E-07
vg0405735993 sf0405731432 4 5735993 2.63E-08 4.18E-06
vg0614117993 sf0614116994 6 14117993 9.75E-08 9.49E-07
vg1209797289 sf1209794699 12 9797289 1.67E-07 3.25E-06
vg0819433740 sf0819431027 8 19433740 8.80E-07 2.65E-07