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 mr1095 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
vg0222724011 sf0222718142 2 22724011 4.25E-56 9.55E-28
vg0906971590 sf0906970590 9 6971590 4.08E-30 NA
vg0526059096 sf0525996516 5 26059096 4.75E-30 NA
vg0920243701 sf0920243220 9 20243701 1.13E-29 NA
vg1007617621 sf1007633230 10 7617621 1.17E-29 NA
vg0526013924 sf0525951344 5 26013924 1.85E-29 3.08E-06
vg0331908781 sf0331901658 3 31908781 4.68E-29 1.18E-06
vg0721347769 sf0721346776 7 21347769 1.53E-28 2.74E-06
vg0222889740 sf0222883871 2 22889740 2.35E-26 5.16E-09
vg0222736300 sf0222730431 2 22736300 5.62E-25 6.30E-11
vg0624076189 sf0624075192 6 24076189 1.27E-24 4.18E-06
vg0434776110 sf0434591001 4 34776110 1.57E-23 1.91E-06
vg0434751283 sf0434566175 4 34751283 6.48E-23 3.84E-06
vg0222725003 sf0222719134 2 22725003 NA 3.58E-10
vg0232358383 sf0232352514 2 32358383 NA 2.54E-07
vg1100554526 sf1100553529 11 554526 NA 3.80E-07
vg0122398282 sf0122397237 1 22398282 NA 1.86E-06
vg1204483091 sf1204482079 12 4483091 NA 2.18E-06
vg1203199238 sf1203198241 12 3199238 NA 2.69E-06
vg0223811992 sf0223783239 2 23811992 NA 2.80E-06
vg0224532813 sf0224526944 2 24532813 NA 2.94E-06
vg0335688200 sf0335681069 3 35688200 NA 2.98E-06
vg0809931541 sf0809930545 8 9931541 NA 6.16E-06