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 mr1542 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
vg0314567323 sf0314566010 3 14567323 1.15E-198 4.58E-88
vg0314577463 sf0314576150 3 14577463 3.23E-139 6.23E-62
vg0903764154 sf0903763154 9 3764154 3.32E-49 NA
vg1226005906 sf1225972300 12 26005906 2.15E-48 NA
vg0520855996 sf0520793437 5 20855996 6.79E-48 NA
vg0726349951 sf0726348957 7 26349951 2.09E-47 NA
vg0314601404 sf0314600091 3 14601404 NA 5.90E-47
vg0314491238 sf0314489926 3 14491238 NA 2.52E-17
vg0314553734 sf0314552422 3 14553734 NA 5.94E-17
vg0314769491 sf0314768178 3 14769491 NA 1.01E-16
vg0314570282 sf0314568969 3 14570282 NA 9.94E-16
vg0314390708 sf0314389397 3 14390708 NA 1.36E-10
vg0314310971 sf0314309660 3 14310971 NA 7.37E-10
vg0314549769 sf0314548457 3 14549769 NA 1.04E-09
vg0314581119 sf0314579806 3 14581119 NA 1.75E-08
vg0314521046 sf0314519734 3 14521046 NA 3.72E-08
vg0314745411 sf0314744098 3 14745411 NA 3.97E-08
vg0314910671 sf0314909318 3 14910671 NA 1.31E-07
vg0314825168 sf0314823855 3 14825168 NA 1.43E-07
vg0500358908 sf0500358908 5 358908 NA 1.50E-07
vg0314840946 sf0314839593 3 14840946 NA 3.10E-07
vg0314644172 sf0314642859 3 14644172 NA 3.88E-07
vg0914764058 sf0914763057 9 14764058 NA 4.61E-07
vg1011635999 sf1011564814 10 11635999 NA 1.29E-06
vg0329522902 sf0329515942 3 29522902 NA 1.30E-06
vg0523419504 sf0523356925 5 23419504 NA 1.50E-06
vg0902628748 sf0902627748 9 2628748 NA 1.69E-06
vg0314646020 sf0314644707 3 14646020 NA 1.79E-06
vg0212583199 sf0212583195 2 12583199 NA 4.89E-06