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 mr1677 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
vg1217066010 sf1217059965 12 17066010 2.62E-10 NA
vg0726932441 sf0726931447 7 26932441 5.54E-10 NA
vg0105134457 sf0105133457 1 5134457 7.58E-10 NA
vg0140491926 sf0140490883 1 40491926 1.63E-09 NA
vg0113814428 sf0113813402 1 13814428 2.31E-09 NA
vg0608286187 sf0608285188 6 8286187 9.80E-08 9.02E-06
vg1020708879 sf1020637358 10 20708879 9.97E-08 6.96E-07
vg0131565439 sf0131564395 1 31565439 1.82E-07 2.51E-06
vg0122825377 sf0122824333 1 22825377 2.82E-07 NA
vg0310177475 sf0310176391 3 10177475 3.66E-07 1.83E-06
vg0130916477 sf0130915433 1 30916477 5.42E-07 NA
vg0504751997 sf0504751974 5 4751997 1.10E-06 NA
vg0406781341 sf0406776786 4 6781341 1.68E-06 NA
vg1127187438 sf1126715825 11 27187438 2.43E-06 4.59E-06
vg0711961663 sf0711960669 7 11961663 NA 2.47E-08
vg1011030483 sf1010959303 10 11030483 NA 3.14E-07
vg0105166660 sf0105165660 1 5166660 NA 1.67E-06
vg0506746775 sf0506746717 5 6746775 NA 4.48E-06