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 mr1805 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
vg1215637989 sf1215635286 12 15637989 1.08E-12 1.54E-08
vg1209245522 sf1209242931 12 9245522 2.55E-12 4.87E-07
vg1100842464 sf1100841465 11 842464 5.21E-11 NA
vg1212118399 sf1212115735 12 12118399 1.52E-10 NA
vg1223877720 sf1223844173 12 23877720 2.28E-10 NA
vg1100988118 sf1100987119 11 988118 6.16E-10 2.96E-06
vg0625068800 sf0625067803 6 25068800 6.56E-10 1.13E-06
vg0328245501 sf0328238555 3 28245501 7.85E-09 6.86E-07
vg0619888183 sf0619887186 6 19888183 1.95E-08 2.61E-06
vg1011360991 sf1011289811 10 11360991 1.09E-06 3.88E-06
vg1127516332 sf1127044719 11 27516332 1.56E-06 5.49E-08
vg0726545921 sf0726544927 7 26545921 1.87E-06 NA
vg0334368026 sf0334360896 3 34368026 2.80E-06 NA
vg0626873273 sf0626872276 6 26873273 4.71E-06 NA
vg0406150023 sf0406145463 4 6150023 NA 3.29E-06
vg0331972225 sf0331965102 3 31972225 NA 4.10E-06