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 mr1435 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 1.33E-42 2.85E-24
vg0217047369 sf0217041499 2 17047369 1.56E-42 6.93E-27
vg0213525745 sf0213525741 2 13525745 3.31E-20 8.05E-09
vg0216462713 sf0216456843 2 16462713 2.75E-17 1.34E-09
vg0216372724 sf0216366854 2 16372724 2.45E-16 1.73E-09
vg0900336793 sf0900335793 9 336793 3.16E-15 2.09E-06
vg0900336799 sf0900335799 9 336799 3.41E-15 8.83E-07
vg0216666516 sf0216660646 2 16666516 3.77E-14 1.23E-06
vg0217377905 sf0217372035 2 17377905 1.27E-13 1.67E-06
vg0217737908 sf0217732038 2 17737908 4.10E-13 6.71E-08
vg1210467503 sf1210464916 12 10467503 8.05E-13 8.96E-08
vg1220237342 sf1220208784 12 20237342 2.03E-11 4.60E-06
vg1210429683 sf1210427096 12 10429683 2.92E-11 NA
vg0216767403 sf0216761533 2 16767403 4.17E-11 6.71E-07
vg0217322508 sf0217316638 2 17322508 2.64E-10 3.99E-07
vg1005364262 sf1005380799 10 5364262 6.93E-09 1.96E-06
vg0411806765 sf0411797476 4 11806765 4.54E-07 1.33E-06
vg0216616335 sf0216610465 2 16616335 5.30E-07 9.35E-07
vg1003674168 sf1003673145 10 3674168 9.87E-07 1.40E-06
vg0525571166 sf0525508587 5 25571166 NA 1.08E-06