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 mr1502 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
vg1218067727 sf1218039163 12 18067727 1.81E-10 NA
vg0141990004 sf0141988961 1 41990004 3.54E-10 NA
vg0329606112 sf0329599152 3 29606112 5.99E-09 NA
vg1121207085 sf1120740963 11 21207085 6.11E-09 NA
vg0702283955 sf0702282956 7 2283955 6.38E-09 NA
vg1119579328 sf1119113016 11 19579328 3.69E-08 3.04E-07
vg0200805927 sf0200805927 2 805927 2.05E-06 NA
vg1010744278 sf1010673099 10 10744278 NA 1.37E-06
vg0420830788 sf0420658831 4 20830788 NA 1.39E-06
vg1000843357 sf1000842333 10 843357 NA 2.23E-06
vg0620234044 sf0620233047 6 20234044 NA 3.13E-06