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 mr1538 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
vg0137881242 sf0137880199 1 37881242 1.37E-92 3.58E-20
vg0717047704 sf0717046711 7 17047704 2.41E-75 2.10E-06
vg0133413972 sf0133412928 1 33413972 9.39E-74 NA
vg0716938954 sf0716937961 7 16938954 8.38E-73 2.00E-06
vg0212084131 sf0212084127 2 12084131 3.76E-72 NA
vg0518861673 sf0518799157 5 18861673 5.80E-72 NA
vg0134277481 sf0134276438 1 34277481 2.02E-71 3.82E-06
vg0715849539 sf0715848546 7 15849539 3.99E-67 2.99E-08
vg1003124968 sf1003123945 10 3124968 NA 1.50E-13
vg1003395810 sf1003394787 10 3395810 NA 1.83E-13
vg0137824518 sf0137823475 1 37824518 NA 1.19E-11
vg0137935177 sf0137934134 1 37935177 NA 1.61E-09
vg0137881863 sf0137880820 1 37881863 NA 2.23E-08
vg1209942861 sf1209940271 12 9942861 NA 1.04E-07
vg0317228312 sf0317227122 3 17228312 NA 9.86E-07
vg1003073690 sf1003072667 10 3073690 NA 1.33E-06
vg0807758908 sf0807757912 8 7758908 NA 1.34E-06
vg1121955589 sf1121489460 11 21955589 NA 1.54E-06
vg0717726887 sf0717725894 7 17726887 NA 1.89E-06
vg1122138317 sf1121672188 11 22138317 NA 2.80E-06