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 mr1557 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
vg0918923523 sf0918922523 9 18923523 2.66E-28 1.82E-09
vg0329602758 sf0329595798 3 29602758 1.68E-27 NA
vg0301666502 sf0301665498 3 1666502 6.64E-26 NA
vg0918891871 sf0918890871 9 18891871 5.11E-25 5.69E-11
vg0918496669 sf0918495668 9 18496669 2.11E-24 1.41E-10
vg0207138890 sf0207138890 2 7138890 1.06E-23 NA
vg1122987844 sf1122521715 11 22987844 2.71E-23 NA
vg1219748904 sf1219720374 12 19748904 1.87E-17 NA
vg0107647091 sf0107646091 1 7647091 5.44E-17 NA
vg0918922771 sf0918921771 9 18922771 NA 7.46E-16
vg0918591036 sf0918590035 9 18591036 NA 2.25E-08
vg0918359050 sf0918358049 9 18359050 NA 7.04E-07
vg1218064709 sf1218036145 12 18064709 NA 1.13E-06
vg0815304114 sf0815301400 8 15304114 NA 1.32E-06
vg0301251510 sf0301250508 3 1251510 NA 3.41E-06
vg0917594974 sf0917593973 9 17594974 NA 3.50E-06
vg0115899007 sf0115897981 1 15899007 NA 4.67E-06