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 mr1089 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
vg0217033543 sf0217027673 2 17033543 2.11E-27 2.25E-23
vg0216721532 sf0216715662 2 16721532 1.08E-14 8.12E-11
vg0812023942 sf0812022947 8 12023942 1.22E-13 1.48E-09
vg0217678234 sf0217672364 2 17678234 1.08E-12 3.36E-08
vg0216223264 sf0216217394 2 16223264 1.09E-11 3.39E-08
vg0216631549 sf0216625679 2 16631549 1.13E-11 1.51E-09
vg0217737425 sf0217731555 2 17737425 1.82E-11 5.22E-08
vg0900336799 sf0900335799 9 336799 1.98E-11 2.62E-08
vg0217797694 sf0217791825 2 17797694 2.34E-11 4.38E-09
vg0216120581 sf0216114711 2 16120581 3.14E-11 5.13E-09
vg0217679949 sf0217674079 2 17679949 9.06E-11 1.13E-08
vg0217677364 sf0217671494 2 17677364 1.00E-10 3.05E-07
vg1210817600 sf1210814966 12 10817600 1.75E-10 3.02E-07
vg0220342684 sf0220336816 2 20342684 1.82E-10 6.56E-08
vg0217328110 sf0217322240 2 17328110 4.14E-10 4.75E-07
vg0216660732 sf0216654862 2 16660732 5.21E-10 5.17E-07
vg0212369213 sf0212369209 2 12369213 7.82E-10 3.41E-07
vg0804587728 sf0804586731 8 4587728 9.49E-10 6.77E-07
vg1005364864 sf1005381401 10 5364864 1.14E-07 7.85E-07
vg0231328780 sf0231322911 2 31328780 2.44E-06 4.74E-07
vg1220237604 sf1220209046 12 20237604 3.74E-06 3.36E-07
vg0132025232 sf0132024188 1 32025232 NA 1.18E-06