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 mr1913 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
vg0222729091 sf0222723222 2 22729091 1.28E-15 2.19E-14
vg0222717596 sf0222711727 2 22717596 2.05E-15 5.36E-15
vg1017582042 sf1017510815 10 17582042 2.12E-08 4.56E-06
vg0725995242 sf0725994248 7 25995242 6.59E-08 NA
vg0222557484 sf0222551615 2 22557484 4.40E-07 1.70E-07
vg0223038405 sf0223032536 2 23038405 1.30E-06 3.55E-06
vg0610608770 sf0610607771 6 10608770 1.45E-06 4.56E-06
vg0825541770 sf0825539056 8 25541770 6.69E-06 2.14E-07
vg1008341354 sf1008270216 10 8341354 NA 2.60E-06
vg0222695295 sf0222689426 2 22695295 NA 2.99E-06
vg1005689748 sf1005706286 10 5689748 NA 3.64E-06
vg0720571909 sf0720570916 7 20571909 NA 5.52E-06