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 mr1129 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
vg0217023211 sf0217017341 2 17023211 1.92E-45 2.21E-29
vg0812023942 sf0812022947 8 12023942 3.84E-20 4.35E-11
vg0900336799 sf0900335799 9 336799 2.97E-17 9.36E-09
vg0213525745 sf0213525741 2 13525745 2.71E-16 3.28E-08
vg0216631549 sf0216625679 2 16631549 7.02E-16 2.15E-10
vg0216219542 sf0216213672 2 16219542 8.49E-15 6.64E-09
vg0217737425 sf0217731555 2 17737425 2.58E-14 1.94E-07
vg1005364262 sf1005380799 10 5364262 2.48E-12 7.22E-10
vg0216661826 sf0216655956 2 16661826 1.75E-10 2.37E-07
vg1210761466 sf1210758830 12 10761466 1.75E-09 7.55E-07
vg0217768536 sf0217762667 2 17768536 2.19E-09 1.37E-07
vg0216773376 sf0216767506 2 16773376 1.36E-08 3.45E-06
vg0213396747 sf0213396743 2 13396747 1.51E-08 2.21E-06
vg0216876069 sf0216870199 2 16876069 1.73E-08 9.34E-07
vg1210368322 sf1210365735 12 10368322 3.69E-07 NA
vg0217338921 sf0217333051 2 17338921 1.65E-06 1.02E-07
vg0230481430 sf0230475561 2 30481430 5.60E-06 NA
vg0505626899 sf0505626837 5 5626899 NA 8.64E-06