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 mr1223 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
vg1012371707 sf1012300522 10 12371707 7.41E-43 3.13E-06
vg1118815887 sf1118349695 11 18815887 1.13E-42 3.32E-06
vg0110444462 sf0110443438 1 10444462 3.49E-41 NA
vg0607100843 sf0607099844 6 7100843 6.37E-41 NA
vg0232531380 sf0232525511 2 32531380 9.76E-41 NA
vg0107647091 sf0107646091 1 7647091 6.38E-38 5.31E-08
vg1215354383 sf1215351681 12 15354383 3.01E-35 3.91E-06
vg1115480914 sf1115017227 11 15480914 NA 2.50E-08
vg1115509243 sf1115045556 11 15509243 NA 5.22E-08
vg1124001841 sf1123535711 11 24001841 NA 3.20E-07
vg0523131395 sf0523068836 5 23131395 NA 3.14E-06
vg0335540142 sf0335533011 3 35540142 NA 3.81E-06
vg0910064812 sf0910063811 9 10064812 NA 4.06E-06
vg0808574594 sf0808573598 8 8574594 NA 9.26E-06