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 mr1995 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
vg0701924178 sf0701923179 7 1924178 8.50E-26 NA
vg0404341374 sf0404336979 4 4341374 3.48E-25 NA
vg0601480019 sf0601479020 6 1480019 3.41E-23 NA
vg1217066010 sf1217059965 12 17066010 4.27E-23 NA
vg0619728473 sf0619727476 6 19728473 1.44E-22 NA
vg0405865352 sf0405860793 4 5865352 1.74E-19 7.00E-07
vg0235145813 sf0235139944 2 35145813 4.38E-18 NA
vg1020747009 sf1020675488 10 20747009 2.72E-17 4.55E-08
vg0803262517 sf0803261520 8 3262517 NA 2.65E-08
vg0601373352 sf0601372353 6 1373352 NA 1.81E-06
vg0420830788 sf0420658831 4 20830788 NA 2.08E-06