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 mr1324 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
vg0101042259 sf0101041259 1 1042259 3.54E-09 NA
vg1218168835 sf1218140271 12 18168835 6.68E-09 7.14E-08
vg0424093648 sf0423908509 4 24093648 7.45E-09 7.47E-06
vg0423899143 sf0423714001 4 23899143 1.24E-08 4.38E-06
vg1218108461 sf1218079897 12 18108461 1.32E-08 1.11E-07
vg0122696302 sf0122695257 1 22696302 3.05E-07 3.01E-06
vg0519892856 sf0519830332 5 19892856 3.52E-07 2.22E-06
vg0122730287 sf0122729243 1 22730287 5.27E-07 2.45E-06
vg1207276357 sf1207273764 12 7276357 9.30E-07 2.57E-06
vg0315818553 sf0315817200 3 15818553 1.48E-06 4.68E-06
vg0919897205 sf0919896724 9 19897205 2.07E-06 NA
vg0501704680 sf0501704664 5 1704680 5.92E-06 2.56E-06
vg0114134418 sf0114133392 1 14134418 7.33E-06 2.38E-06