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
vg0137855094 sf0137854051 1 37855094 4.12E-142 9.99E-27
vg0107725970 sf0107724970 1 7725970 2.49E-111 NA
vg0133397324 sf0133396280 1 33397324 1.40E-109 8.32E-06
vg1114200135 sf1113736456 11 14200135 2.52E-108 NA
vg0107608673 sf0107607673 1 7608673 2.85E-108 5.52E-08
vg0518842252 sf0518779736 5 18842252 1.48E-106 NA
vg1003392770 sf1003391747 10 3392770 NA 1.94E-14
vg1003374258 sf1003373235 10 3374258 NA 4.74E-14
vg1003432879 sf1003431856 10 3432879 NA 1.02E-12
vg0137854833 sf0137853790 1 37854833 NA 2.26E-11
vg0137833133 sf0137832090 1 37833133 NA 5.74E-09
vg0137834227 sf0137833184 1 37834227 NA 9.55E-09
vg1003491099 sf1003490076 10 3491099 NA 2.94E-07
vg0135237999 sf0135236956 1 35237999 NA 3.46E-07
vg0127969087 sf0127968043 1 27969087 NA 1.77E-06
vg0901391504 sf0901390504 9 1391504 NA 2.49E-06
vg0217468639 sf0217462769 2 17468639 NA 2.61E-06
vg0225271952 sf0225266083 2 25271952 NA 2.80E-06
vg0717727677 sf0717726684 7 17727677 NA 4.39E-06
vg1120474541 sf1120008466 11 20474541 NA 4.51E-06