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 mr1270 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
vg0504543759 sf0504543736 5 4543759 4.65E-33 NA
vg0708978860 sf0708977866 7 8978860 5.27E-33 2.12E-06
vg0520607066 sf0520544507 5 20607066 5.90E-33 NA
vg1201968520 sf1201967518 12 1968520 7.95E-33 NA
vg0317950141 sf0317948923 3 17950141 1.56E-32 5.15E-06
vg0317274577 sf0317273387 3 17274577 NA 9.17E-07
vg1004059501 sf1004058477 10 4059501 NA 9.81E-07
vg0422487581 sf0422302468 4 22487581 NA 4.10E-06
vg0715014794 sf0715013801 7 15014794 NA 4.31E-06