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 mr1875 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
vg0123633523 sf0123632479 1 23633523 2.55E-13 NA
vg1126584071 sf1126112486 11 26584071 2.61E-12 4.25E-09
vg0619445566 sf0619444569 6 19445566 4.20E-12 NA
vg1125786354 sf1125320275 11 25786354 5.10E-12 2.01E-06
vg0307490311 sf0307489249 3 7490311 8.65E-12 NA
vg0122413633 sf0122412588 1 22413633 5.50E-11 4.70E-06
vg0122413949 sf0122412904 1 22413949 1.67E-10 2.84E-06
vg1126497827 sf1126026241 11 26497827 6.99E-10 6.84E-07
vg1121472427 sf1121006304 11 21472427 1.09E-08 NA
vg0526250453 sf0526187817 5 26250453 2.82E-07 NA
vg0141059481 sf0141058438 1 41059481 NA 1.21E-06
vg0123676188 sf0123675144 1 23676188 NA 1.96E-06
vg1203635072 sf1203634071 12 3635072 NA 6.58E-06