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 mr1109 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
vg0216752678 sf0216746808 2 16752678 9.03E-56 2.96E-29
vg0217047369 sf0217041499 2 17047369 1.72E-55 9.36E-31
vg0213525745 sf0213525741 2 13525745 5.69E-23 4.14E-08
vg0216370112 sf0216364242 2 16370112 9.94E-21 2.82E-07
vg0900337327 sf0900336327 9 337327 2.37E-20 2.22E-08
vg0900336799 sf0900335799 9 336799 7.05E-20 7.41E-09
vg0812023942 sf0812022947 8 12023942 8.30E-19 2.35E-06
vg0216357484 sf0216351614 2 16357484 1.01E-18 6.05E-08
vg0216278300 sf0216272430 2 16278300 2.47E-17 2.91E-06
vg0217737734 sf0217731864 2 17737734 4.82E-14 2.58E-07
vg1208648368 sf1208645775 12 8648368 8.21E-12 4.95E-06
vg0525571166 sf0525508587 5 25571166 2.98E-11 6.89E-09
vg0217809768 sf0217803899 2 17809768 3.10E-11 8.37E-07
vg0525568162 sf0525505583 5 25568162 3.12E-11 1.05E-07
vg0216032860 sf0216026990 2 16032860 8.58E-11 3.49E-06
vg1005364262 sf1005380799 10 5364262 1.69E-10 1.27E-09
vg0216876069 sf0216870199 2 16876069 4.11E-09 1.77E-08
vg0217291492 sf0217285622 2 17291492 NA 2.52E-06
vg0811120484 sf0811119489 8 11120484 NA 3.35E-06