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 mr1379 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
vg0216691537 sf0216685667 2 16691537 2.29E-08 2.29E-08
vg0217018976 sf0217013106 2 17018976 2.18E-07 2.18E-07
vg0235128530 sf0235122661 2 35128530 2.30E-07 2.30E-07
vg0406877935 sf0406873380 4 6877935 5.92E-07 5.92E-07
vg0620348476 sf0620347479 6 20348476 6.62E-07 6.62E-07
vg0334850928 sf0334843798 3 34850928 1.29E-06 1.29E-06
vg1005364262 sf1005380799 10 5364262 1.69E-06 1.69E-06
vg0712648528 sf0712647535 7 12648528 2.65E-06 2.65E-06
vg0142475082 sf0142474038 1 42475082 3.13E-06 3.13E-06
vg0406233178 sf0406228618 4 6233178 3.42E-06 3.42E-06
vg0406828836 sf0406824281 4 6828836 3.99E-06 3.99E-06
vg0335000939 sf0334993809 3 35000939 4.29E-06 4.29E-06
vg0809713199 sf0809712203 8 9713199 4.35E-06 4.35E-06
vg0142642319 sf0142641275 1 42642319 8.68E-06 8.68E-06