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 mr1208 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
vg0922290793 sf0922290312 9 22290793 3.16E-45 4.63E-06
vg0304906107 sf0304905109 3 4906107 3.11E-44 NA
vg0420339575 sf0420167619 4 20339575 1.42E-43 NA
vg0905168183 sf0905167183 9 5168183 7.35E-43 NA
vg0612891413 sf0612890414 6 12891413 1.23E-42 NA
vg0922081469 sf0922080988 9 22081469 4.71E-42 1.65E-11
vg0902251270 sf0902250270 9 2251270 1.62E-37 1.71E-07
vg0901841716 sf0901840716 9 1841716 NA 9.37E-09
vg0902470420 sf0902469420 9 2470420 NA 2.80E-07
vg1123192315 sf1122726186 11 23192315 NA 5.40E-07
vg0901136591 sf0901135591 9 1136591 NA 7.26E-07
vg1011932223 sf1011861038 10 11932223 NA 7.63E-07
vg0212840859 sf0212840855 2 12840859 NA 1.01E-06
vg0904455249 sf0904454249 9 4455249 NA 1.48E-06
vg0106366763 sf0106365763 1 6366763 NA 1.83E-06
vg0601621819 sf0601620820 6 1621819 NA 3.62E-06
vg0402172596 sf0402168191 4 2172596 NA 4.89E-06