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 mr1134 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
vg1107375253 sf1107370998 11 7375253 3.92E-10 4.96E-10
vg0813628932 sf0813626217 8 13628932 6.23E-10 7.24E-06
vg0900072657 sf0900071657 9 72657 7.74E-10 9.90E-06
vg0814303967 sf0814301253 8 14303967 4.76E-09 NA
vg0810301653 sf0810300657 8 10301653 1.21E-08 NA
vg0138434066 sf0138433023 1 38434066 3.50E-08 1.58E-06
vg0810921871 sf0810920876 8 10921871 8.21E-08 7.00E-07
vg1119719316 sf1119253004 11 19719316 1.23E-07 3.63E-07
vg0801869183 sf0801868186 8 1869183 1.56E-07 2.99E-06
vg0421397191 sf0421225244 4 21397191 1.70E-06 2.21E-06
vg1226233110 sf1226199504 12 26233110 2.28E-06 1.00E-06
vg0617703446 sf0617702449 6 17703446 5.30E-06 NA
vg0816234557 sf0816231843 8 16234557 8.21E-06 4.33E-07
vg0217649884 sf0217644014 2 17649884 NA 8.21E-07
vg0138424728 sf0138423685 1 38424728 NA 2.29E-06
vg0816234574 sf0816231860 8 16234574 NA 2.80E-06
vg0334486785 sf0334479655 3 34486785 NA 3.39E-06
vg0334513208 sf0334506078 3 34513208 NA 5.13E-06