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 mr1195 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
vg0507197516 sf0507197458 5 7197516 7.45E-25 3.84E-13
vg0507132804 sf0507132746 5 7132804 1.29E-24 2.96E-13
vg0527367835 sf0527305191 5 27367835 8.11E-19 NA
vg0524250221 sf0524187640 5 24250221 3.55E-15 NA
vg0406502844 sf0406498287 4 6502844 2.21E-14 NA
vg0525537287 sf0525474708 5 25537287 7.22E-14 2.55E-07
vg0525615548 sf0525552969 5 25615548 2.60E-13 2.85E-07
vg0417713254 sf0417541292 4 17713254 6.64E-13 NA
vg0111338686 sf0111337662 1 11338686 NA 2.26E-06
vg1215972646 sf1215969942 12 15972646 NA 3.32E-06