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 mr1250 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
vg0216657284 sf0216651414 2 16657284 4.34E-12 6.90E-07
vg0216627796 sf0216621926 2 16627796 3.59E-11 5.52E-07
vg1004756810 sf1004773347 10 4756810 3.86E-10 2.64E-06
Unknow sf1004105309 Unknow Unknow 2.50E-09 NA
vg0431516737 sf0431331636 4 31516737 5.91E-09 NA
vg0121871143 sf0121870098 1 21871143 6.52E-09 2.87E-06
vg1009645414 sf1009574235 10 9645414 6.88E-09 4.30E-07
vg0216680498 sf0216674628 2 16680498 9.58E-09 8.20E-06
vg0216677984 sf0216672114 2 16677984 1.03E-08 4.82E-06
vg0431515534 sf0431330433 4 31515534 1.63E-08 6.50E-08
vg1009262901 sf1009191722 10 9262901 2.11E-08 6.67E-07
vg0319397200 sf0319395711 3 19397200 2.14E-08 1.92E-06
vg1009327768 sf1009256589 10 9327768 2.38E-08 1.22E-06
vg0407668419 sf0407663686 4 7668419 7.06E-08 3.87E-06
vg0223422604 sf0223416735 2 23422604 1.17E-07 NA
vg0412457639 sf0412448354 4 12457639 1.69E-07 4.02E-06
vg1009262784 sf1009191605 10 9262784 2.13E-07 8.59E-07
vg0429843384 sf0429658254 4 29843384 4.08E-07 NA
vg0427400029 sf0427214893 4 27400029 1.71E-06 4.07E-06