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 mr1251 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
vg0216956622 sf0216950752 2 16956622 1.11E-42 2.74E-24
vg0217047369 sf0217041499 2 17047369 1.29E-42 6.11E-27
vg0213525745 sf0213525741 2 13525745 3.10E-20 7.87E-09
vg0216462713 sf0216456843 2 16462713 1.77E-17 9.43E-10
vg0216372724 sf0216366854 2 16372724 1.69E-16 1.30E-09
vg0900336793 sf0900335793 9 336793 2.70E-15 2.14E-06
vg0900336799 sf0900335799 9 336799 2.99E-15 9.02E-07
vg0216666516 sf0216660646 2 16666516 2.22E-14 9.39E-07
vg0217377905 sf0217372035 2 17377905 7.60E-14 1.41E-06
vg1210467503 sf1210464916 12 10467503 1.00E-12 1.10E-07
vg0217737900 sf0217732030 2 17737900 4.44E-12 5.67E-08
vg0216767403 sf0216761533 2 16767403 1.63E-11 3.49E-07
vg1220237342 sf1220208784 12 20237342 2.30E-11 4.87E-06
vg0217322508 sf0217316638 2 17322508 3.18E-10 4.62E-07
vg1005364262 sf1005380799 10 5364262 8.31E-09 2.33E-06
vg0411806765 sf0411797476 4 11806765 5.04E-07 1.54E-06
vg0216616335 sf0216610465 2 16616335 5.15E-07 7.63E-07
vg0525571166 sf0525508587 5 25571166 NA 6.77E-07
vg1003674168 sf1003673145 10 3674168 NA 1.48E-06