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 mr1484 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
vg1125118463 sf1124652303 11 25118463 3.34E-29 4.86E-29
vg1124991220 sf1124525060 11 24991220 2.57E-08 1.81E-11
vg1124966900 sf1124500740 11 24966900 2.68E-08 7.91E-12
vg1124969445 sf1124503285 11 24969445 3.07E-08 8.31E-08
vg1128439104 sf1127915883 11 28439104 3.08E-08 2.16E-06
vg1125432444 sf1124966283 11 25432444 5.89E-08 1.52E-06
vg1125555604 sf1125089443 11 25555604 9.27E-08 4.52E-07
vg0814644208 sf0814641494 8 14644208 2.07E-07 2.89E-07
vg1124875808 sf1124409648 11 24875808 2.51E-06 1.06E-07
vg0613084781 sf0613083782 6 13084781 8.61E-06 4.56E-06
vg1124948132 sf1124481972 11 24948132 NA 6.96E-07
vg1125343326 sf1124877166 11 25343326 NA 1.65E-06
vg1125256284 sf1124790124 11 25256284 NA 4.15E-06
vg0208287795 sf0208287794 2 8287795 NA 4.77E-06