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 mr1860 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
vg0916242445 sf0916241444 9 16242445 7.77E-23 4.40E-12
vg0918158744 sf0918157743 9 18158744 7.77E-23 1.88E-11
vg1022093624 sf1022022099 10 22093624 5.66E-15 1.82E-06
vg1218123524 sf1218094960 12 18123524 7.43E-14 NA
vg1104302810 sf1104298712 11 4302810 9.96E-14 NA
vg0821655390 sf0821652677 8 21655390 1.59E-13 NA
vg0417900657 sf0417728698 4 17900657 2.18E-11 2.14E-06
vg0507006230 sf0507006172 5 7006230 2.30E-11 NA
vg0332412088 sf0332404960 3 32412088 2.45E-11 1.77E-06
vg0913952823 sf0913951822 9 13952823 1.09E-09 2.67E-06
vg0810394812 sf0810393816 8 10394812 NA 1.21E-06
vg0333612911 sf0333605781 3 33612911 NA 1.73E-06
vg0216477558 sf0216471688 2 16477558 NA 1.82E-06
vg0714688578 sf0714687585 7 14688578 NA 4.62E-06
vg0315272708 sf0315271355 3 15272708 NA 4.70E-06