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 mr1935 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
vg0921387658 sf0921387177 9 21387658 6.13E-10 6.14E-10
vg0721028689 sf0721027696 7 21028689 7.14E-09 7.14E-09
vg0114145969 sf0114144943 1 14145969 7.90E-08 7.90E-08
vg0706618955 sf0706617960 7 6618955 1.13E-07 1.13E-07
vg0622383329 sf0622382332 6 22383329 4.95E-07 4.95E-07
vg0233727690 sf0233721821 2 33727690 5.16E-07 5.16E-07
vg0203256467 sf0203256465 2 3256467 5.58E-07 5.58E-07
vg1227007533 sf1226973932 12 27007533 6.02E-07 6.02E-07
vg0128471692 sf0128470647 1 28471692 8.38E-07 8.38E-07
vg0225789722 sf0225783853 2 25789722 1.08E-06 1.08E-06
vg0207211946 sf0207211946 2 7211946 1.19E-06 1.19E-06
vg0135645855 sf0135644812 1 35645855 1.26E-06 1.26E-06
vg1206202617 sf1206201507 12 6202617 1.76E-06 1.76E-06
vg0139276484 sf0139275441 1 39276484 1.76E-06 1.76E-06
vg0803364457 sf0803363460 8 3364457 2.80E-06 2.80E-06
vg0306293313 sf0306292313 3 6293313 3.30E-06 3.30E-06
vg0105393860 sf0105392860 1 5393860 3.67E-06 3.67E-06
vg0910076716 sf0910075715 9 10076716 4.45E-06 4.45E-06
vg0211479975 sf0211479971 2 11479975 4.67E-06 4.67E-06
vg1200437573 sf1200436573 12 437573 4.97E-06 4.97E-06