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 mr1152 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
vg0815685263 sf0815682549 8 15685263 2.75E-44 7.66E-07
vg0815688098 sf0815685384 8 15688098 3.70E-44 1.97E-07
vg0229918346 sf0229912477 2 29918346 6.86E-44 NA
vg1227329375 sf1227295775 12 27329375 2.61E-43 NA
vg0916109112 sf0916108111 9 16109112 4.27E-43 NA
vg0214920595 sf0214914725 2 14920595 5.32E-43 NA
vg0229966627 sf0229960758 2 29966627 1.87E-41 NA
vg0626516039 sf0626515042 6 26516039 8.96E-41 NA
vg0139928356 sf0139927313 1 39928356 1.96E-39 2.45E-07
vg1012062825 sf1011991640 10 12062825 4.63E-39 NA
vg0130736176 sf0130735132 1 30736176 NA 4.54E-16
vg0130813657 sf0130812613 1 30813657 NA 7.06E-10
vg0135821566 sf0135820523 1 35821566 NA 9.89E-08
vg0113096184 sf0113095158 1 13096184 NA 3.10E-07
vg0131033386 sf0131032342 1 31033386 NA 7.89E-07
vg0130856412 sf0130855368 1 30856412 NA 1.59E-06
vg0122013723 sf0122012678 1 22013723 NA 2.86E-06
vg0132820024 sf0132818980 1 32820024 NA 3.78E-06
vg1226956034 sf1226922433 12 26956034 NA 4.25E-06
vg0401719894 sf0401715443 4 1719894 NA 4.84E-06
vg0432523363 sf0432338255 4 32523363 NA 5.66E-06