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 mr1670 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
vg0138132963 sf0138131920 1 38132963 2.15E-52 3.13E-17
vg1119493431 sf1119027119 11 19493431 3.93E-44 2.64E-08
vg1119500504 sf1119034192 11 19500504 1.61E-43 1.45E-08
vg0321437873 sf0321436383 3 21437873 4.03E-40 NA
vg0107527213 sf0107526213 1 7527213 4.18E-40 7.77E-06
vg0214612807 sf0214606937 2 14612807 5.28E-40 NA
vg1223765446 sf1223731899 12 23765446 6.64E-34 5.02E-06
vg0400407662 sf0400406660 4 407662 NA 4.16E-13
vg0225843299 sf0225837430 2 25843299 NA 6.32E-08
vg0402061955 sf0402057550 4 2061955 NA 1.54E-07
vg1222877771 sf1222844211 12 22877771 NA 1.98E-07
vg0401948084 sf0401943680 4 1948084 NA 2.80E-07
vg1216529599 sf1216526892 12 16529599 NA 4.88E-07
vg0402417093 sf0402412689 4 2417093 NA 5.99E-07
vg1016835838 sf1016764610 10 16835838 NA 1.24E-06
vg0400441736 sf0400440734 4 441736 NA 2.40E-06
vg0401888324 sf0401883920 4 1888324 NA 3.02E-06
vg1005691241 sf1005707779 10 5691241 NA 3.27E-06
vg1223765454 sf1223731907 12 23765454 NA 4.08E-06