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 mr1497 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
vg0235013338 sf0235007469 2 35013338 3.85E-11 NA
vg0818652211 sf0818649498 8 18652211 1.21E-10 NA
vg1219566901 sf1219538371 12 19566901 2.21E-10 NA
vg1227148815 sf1227115214 12 27148815 3.50E-10 NA
vg0102845480 sf0102844480 1 2845480 4.47E-10 NA
vg0434768530 sf0434583421 4 34768530 1.56E-07 1.25E-07
vg1104369663 sf1104365565 11 4369663 3.36E-07 NA
vg0622673582 sf0622672585 6 22673582 3.61E-06 NA
vg1219176479 sf1219147949 12 19176479 5.50E-06 4.16E-06
vg0711196957 sf0711195963 7 11196957 9.65E-06 2.61E-06
vg0232481318 sf0232475449 2 32481318 NA 4.15E-06
vg1209697699 sf1209708295 12 9697699 NA 4.64E-06
vg0101344528 sf0101343528 1 1344528 NA 4.65E-06
vg0308567901 sf0308566839 3 8567901 NA 7.77E-06