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 mr1490 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
vg1215967035 sf1215964331 12 15967035 4.13E-49 2.55E-25
vg0500829493 sf0500829475 5 829493 2.83E-19 NA
vg1212873997 sf1212871336 12 12873997 1.59E-17 1.35E-06
vg1011512136 sf1011440955 10 11512136 2.59E-17 4.82E-08
vg0811139003 sf0811138008 8 11139003 5.93E-17 NA
vg1005031656 sf1005048193 10 5031656 8.54E-15 7.46E-07
vg1215271044 sf1215268342 12 15271044 8.31E-13 6.56E-07
vg1018579412 sf1018507969 10 18579412 9.07E-13 3.00E-06
vg1218663003 sf1218634438 12 18663003 1.54E-11 4.76E-07
vg1215876237 sf1215873533 12 15876237 2.30E-11 1.27E-06
vg1006587700 sf1006603323 10 6587700 3.77E-11 7.22E-07
vg1215852700 sf1215849996 12 15852700 NA 6.63E-11
vg1022588644 sf1022517118 10 22588644 NA 4.07E-08
vg1206197673 sf1206196564 12 6197673 NA 2.35E-07
vg1216463200 sf1216460493 12 16463200 NA 2.72E-07
vg1208048502 sf1208045908 12 8048502 NA 2.76E-07
vg0901555655 sf0901554655 9 1555655 NA 1.05E-06
vg0432732386 sf0432547273 4 32732386 NA 2.49E-06