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 mr1062 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
vg0406288626 sf0406284066 4 6288626 1.53E-19 2.30E-15
vg0410515163 sf0410505862 4 10515163 3.16E-15 5.76E-10
vg0803326358 sf0803325361 8 3326358 3.00E-14 1.07E-09
vg0605723364 sf0605722365 6 5723364 4.28E-12 1.01E-06
vg0405780712 sf0405776151 4 5780712 6.30E-12 1.06E-08
vg0334326919 sf0334319789 3 34326919 3.10E-11 1.54E-06
vg0127557410 sf0127556366 1 27557410 4.56E-11 5.03E-07
vg1209001736 sf1208999144 12 9001736 5.86E-11 4.89E-07
vg0131616560 sf0131615516 1 31616560 8.78E-11 6.73E-07
vg0405727925 sf0405723364 4 5727925 1.17E-10 9.91E-09
vg0907785140 sf0907784140 9 7785140 1.24E-10 1.39E-06
vg0809622371 sf0809621375 8 9622371 1.72E-10 1.41E-06
vg0218297603 sf0218291734 2 18297603 4.79E-10 6.21E-07
vg0626070193 sf0626069196 6 26070193 6.07E-10 5.54E-07
vg0907843042 sf0907842042 9 7843042 9.41E-10 6.30E-06
vg0907746322 sf0907745322 9 7746322 1.51E-09 4.31E-06
vg1005835090 sf1005851628 10 5835090 2.16E-09 3.17E-06
vg1111482820 sf1111477137 11 11482820 2.07E-08 3.06E-06
vg0806194312 sf0806193317 8 6194312 2.44E-07 3.34E-06
vg0405898112 sf0405893553 4 5898112 1.28E-06 4.68E-06
vg1000221774 sf1000220774 10 221774 3.16E-06 NA
vg0106157133 sf0106156133 1 6157133 4.43E-06 4.51E-06
vg1119545646 sf1119079334 11 19545646 NA 3.69E-06
vg0920292378 sf0920291897 9 20292378 NA 4.46E-06