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 mr1120 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 5.08E-16 1.67E-12
vg0336193973 sf0336186899 3 36193973 3.75E-14 3.41E-11
vg0421388196 sf0421216249 4 21388196 4.35E-13 2.70E-09
vg0728000317 sf0727999324 7 28000317 1.09E-12 3.67E-09
vg0504720198 sf0504720175 5 4720198 7.83E-12 7.01E-08
vg1001348300 sf1001347277 10 1348300 8.89E-12 7.68E-08
vg0308535729 sf0308534667 3 8535729 3.32E-11 1.72E-07
vg1126461419 sf1125989832 11 26461419 1.04E-10 8.53E-08
vg0334827866 sf0334820736 3 34827866 1.45E-10 3.39E-08
vg0906313471 sf0906312471 9 6313471 1.75E-10 8.84E-09
vg1016339056 sf1016267832 10 16339056 1.93E-10 2.03E-07
vg1117137503 sf1116671355 11 17137503 3.49E-10 1.42E-08
vg0315684189 sf0315682836 3 15684189 5.98E-10 8.27E-07
vg1201867679 sf1201866676 12 1867679 9.38E-10 2.37E-07
vg0424049928 sf0423864789 4 24049928 1.16E-09 8.82E-07
vg0819421680 sf0819418967 8 19421680 4.52E-09 1.32E-08
vg1002009944 sf1002008921 10 2009944 8.89E-09 4.58E-07
vg0819366916 sf0819364203 8 19366916 1.68E-08 4.36E-07
vg0714480545 sf0714479552 7 14480545 6.89E-07 4.08E-07
vg0219292377 sf0219286509 2 19292377 6.93E-07 5.44E-07
vg0122176305 sf0122175260 1 22176305 1.95E-06 1.28E-07
vg1204324619 sf1204323607 12 4324619 NA 2.32E-06