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 mr1301 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
vg0417238354 sf0417066395 4 17238354 2.97E-55 4.28E-30
vg0519939017 sf0519876493 5 19939017 3.58E-37 3.50E-20
vg0406910836 sf0406906103 4 6910836 1.38E-35 5.25E-16
vg0410681849 sf0410672551 4 10681849 1.64E-32 2.58E-14
vg0401797174 sf0401792769 4 1797174 2.40E-32 9.74E-12
vg0309190281 sf0309189217 3 9190281 1.30E-31 7.44E-12
vg0403055424 sf0403051028 4 3055424 1.85E-31 3.09E-15
vg0707065048 sf0707064053 7 7065048 4.24E-31 3.42E-09
vg0211588654 sf0211588650 2 11588654 3.80E-30 4.26E-13
vg0722183786 sf0722182793 7 22183786 7.42E-29 4.16E-11
vg0801480069 sf0801479071 8 1480069 1.46E-27 3.09E-11
vg0817661668 sf0817658955 8 17661668 3.01E-27 1.12E-11
vg0111490485 sf0111489461 1 11490485 2.03E-26 1.11E-11
vg0903433897 sf0903432897 9 3433897 8.63E-26 2.32E-11
vg0506590630 sf0506590571 5 6590630 1.22E-25 7.01E-09
vg0823849578 sf0823846864 8 23849578 1.78E-25 4.61E-09
vg0614481201 sf0614480202 6 14481201 4.79E-24 7.57E-11
vg0409481218 sf0409471916 4 9481218 NA 3.55E-10
vg0518975375 sf0518912859 5 18975375 NA 2.27E-09
vg1013381694 sf1013310464 10 13381694 NA 4.55E-09
vg0430364199 sf0430179076 4 30364199 NA 8.62E-09
vg0103416327 sf0103415327 1 3416327 NA 2.77E-06
vg0502284343 sf0502284318 5 2284343 NA 6.78E-06
vg1202398699 sf1202397700 12 2398699 NA 9.89E-06