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 mr1119 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
vg0421387824 sf0421215877 4 21387824 9.75E-19 3.21E-14
vg0728000317 sf0727999324 7 28000317 4.25E-16 2.25E-11
vg0336193973 sf0336186899 3 36193973 5.08E-16 7.38E-12
vg1001348300 sf1001347277 10 1348300 8.92E-15 3.75E-10
vg0308535729 sf0308534667 3 8535729 2.11E-14 1.60E-09
vg0504720198 sf0504720175 5 4720198 6.34E-14 4.61E-09
vg1016339056 sf1016267832 10 16339056 6.88E-13 6.74E-09
vg1201867679 sf1201866676 12 1867679 2.61E-11 5.34E-08
vg0424049928 sf0423864789 4 24049928 4.31E-11 1.76E-07
vg0906313471 sf0906312471 9 6313471 5.50E-11 3.57E-08
vg0334827866 sf0334820736 3 34827866 6.48E-11 1.73E-07
vg1126461419 sf1125989832 11 26461419 7.14E-11 1.23E-07
vg0515214258 sf0515156800 5 15214258 1.70E-10 2.95E-07
vg1117137503 sf1116671355 11 17137503 2.05E-10 1.18E-08
vg0222717674 sf0222711805 2 22717674 4.65E-10 3.33E-07
vg1227451463 sf1227417863 12 27451463 7.99E-09 4.91E-08
vg1205542061 sf1205541047 12 5542061 1.02E-08 2.41E-07
vg0219292377 sf0219286509 2 19292377 1.97E-07 2.59E-07
vg0819421680 sf0819418967 8 19421680 1.99E-07 5.31E-07
vg1208630676 sf1208628083 12 8630676 NA 6.32E-08