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 mr1645 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
vg1226043015 sf1226009409 12 26043015 3.15E-45 NA
vg0917434356 sf0917433355 9 17434356 3.66E-45 NA
vg1014220368 sf1014149134 10 14220368 8.12E-45 NA
vg0215705748 sf0215699878 2 15705748 4.50E-44 NA
vg0714987440 sf0714986447 7 14987440 4.73E-44 NA
vg1218022526 sf1217993962 12 18022526 NA 8.07E-10
vg0119895987 sf0119894942 1 19895987 NA 7.30E-08
vg1217862267 sf1217833701 12 17862267 NA 1.40E-07
vg0410434829 sf0410425528 4 10434829 NA 1.21E-06
vg0335630368 sf0335623237 3 35630368 NA 2.39E-06
vg0517141494 sf0517081135 5 17141494 NA 2.44E-06
vg0813540176 sf0813537729 8 13540176 NA 2.65E-06
vg1216728644 sf1216722598 12 16728644 NA 2.82E-06
vg0715411335 sf0715410342 7 15411335 NA 3.73E-06
vg0910414094 sf0910413093 9 10414094 NA 4.34E-06
vg1127533551 sf1127061938 11 27533551 NA 4.70E-06
vg1204078883 sf1204077871 12 4078883 NA 4.80E-06