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 mr1092 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
vg0916109112 sf0916108111 9 16109112 7.63E-45 NA
vg1227386785 sf1227353185 12 27386785 4.13E-44 NA
vg0815685263 sf0815682549 8 15685263 5.68E-44 8.38E-07
vg0620606045 sf0620605048 6 20606045 7.83E-44 NA
vg0815688098 sf0815685384 8 15688098 8.99E-44 3.00E-07
vg0211547954 sf0211547950 2 11547954 1.19E-43 NA
vg0139928356 sf0139927313 1 39928356 7.70E-41 1.51E-08
vg0130670983 sf0130669939 1 30670983 NA 8.39E-17
vg0130826614 sf0130825570 1 30826614 NA 1.18E-09
vg0131033386 sf0131032342 1 31033386 NA 1.80E-08
vg1115489572 sf1115025885 11 15489572 NA 1.53E-07
vg0130856412 sf0130855368 1 30856412 NA 3.22E-07
vg0135821566 sf0135820523 1 35821566 NA 6.89E-07
vg0726380549 sf0726379555 7 26380549 NA 8.33E-07
vg0818200735 sf0818198022 8 18200735 NA 2.11E-06
vg0113096184 sf0113095158 1 13096184 NA 2.26E-06
vg0311737098 sf0311735816 3 11737098 NA 2.52E-06
vg0139977615 sf0139976572 1 39977615 NA 3.05E-06
vg0432523363 sf0432338255 4 32523363 NA 3.34E-06
vg0223422615 sf0223416746 2 23422615 NA 3.81E-06