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 mr1846 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
vg0411404313 sf0411395016 4 11404313 6.78E-54 1.89E-16
vg0408524000 sf0408519273 4 8524000 2.37E-49 1.18E-11
vg0407264314 sf0407259584 4 7264314 8.97E-47 1.86E-12
vg0414006438 sf0413997153 4 14006438 1.15E-36 2.19E-06
vg0614462540 sf0614461541 6 14462540 8.55E-31 NA
vg0414021996 sf0414012711 4 14021996 2.41E-30 2.54E-07
vg0402378441 sf0402374036 4 2378441 1.82E-23 NA
vg0614459942 sf0614458943 6 14459942 1.31E-22 3.06E-07
vg0905314628 sf0905313628 9 5314628 5.70E-22 6.99E-07
vg1110033720 sf1110028297 11 10033720 8.10E-18 9.85E-07
vg0409842483 sf0409833181 4 9842483 4.59E-16 4.03E-06
vg0410073312 sf0410064010 4 10073312 4.84E-16 1.58E-14
vg0407262262 sf0407257532 4 7262262 5.66E-16 5.69E-16
vg0411807924 sf0411798635 4 11807924 8.71E-16 1.59E-06
vg0414013336 sf0414004051 4 14013336 8.92E-14 3.45E-09
vg0812791309 sf0812789134 8 12791309 2.25E-13 1.18E-08
vg0601659985 sf0601658986 6 1659985 NA 6.04E-08
vg0805968808 sf0805967811 8 5968808 NA 4.96E-07
vg0411635886 sf0411626592 4 11635886 NA 1.00E-06
vg0311297778 sf0311296496 3 11297778 NA 1.70E-06
vg0209217878 sf0209217876 2 9217878 NA 1.96E-06
vg0206334099 sf0206334099 2 6334099 NA 2.39E-06
vg0332994931 sf0332987801 3 32994931 NA 2.58E-06
vg0905315058 sf0905314058 9 5315058 NA 3.26E-06