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 mr1412 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
vg0102103204 sf0102102204 1 2103204 3.35E-08 3.36E-08
vg0805992743 sf0805991746 8 5992743 8.75E-08 8.69E-08
vg0220342715 sf0220336847 2 20342715 5.80E-07 5.77E-07
vg0122965976 sf0122964932 1 22965976 9.53E-07 9.55E-07
vg1118368019 sf1117901877 11 18368019 9.87E-07 9.88E-07
vg0105761092 sf0105760092 1 5761092 1.05E-06 1.05E-06
vg0307132377 sf0307131375 3 7132377 1.18E-06 1.18E-06
vg1221999258 sf1221965805 12 21999258 1.56E-06 1.56E-06
vg0819439794 sf0819437081 8 19439794 1.82E-06 1.83E-06
vg0527921996 sf0527859353 5 27921996 2.70E-06 2.70E-06
vg0410770678 sf0410761379 4 10770678 2.75E-06 2.75E-06
vg1219176458 sf1219147928 12 19176458 2.84E-06 2.85E-06
vg0907430352 sf0907429352 9 7430352 2.96E-06 2.97E-06
vg0131567146 sf0131566102 1 31567146 3.02E-06 3.03E-06
vg0102809057 sf0102808057 1 2809057 3.12E-06 3.13E-06
vg1217569480 sf1217563435 12 17569480 3.80E-06 3.81E-06
vg0421294092 sf0421122146 4 21294092 4.17E-06 4.18E-06
vg0816931318 sf0816928604 8 16931318 4.29E-06 4.29E-06
vg1214134657 sf1214131997 12 14134657 4.32E-06 4.33E-06
vg0819855776 sf0819853063 8 19855776 4.71E-06 4.72E-06