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 mr1861 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
vg0222725881 sf0222720012 2 22725881 8.00E-44 1.88E-26
vg0222738038 sf0222732169 2 22738038 8.16E-43 1.50E-27
vg0223908657 sf0223902788 2 23908657 1.12E-16 1.31E-07
vg0223537448 sf0223531579 2 23537448 6.45E-16 1.58E-09
vg0223914026 sf0223908157 2 23914026 3.04E-15 7.53E-08
vg0224236356 sf0224230487 2 24236356 2.53E-13 9.11E-09
vg0229592697 sf0229586828 2 29592697 3.85E-13 NA
vg0120478712 sf0120477667 1 20478712 6.05E-13 NA
vg0224293556 sf0224287687 2 24293556 2.21E-12 6.20E-09
vg0121061296 sf0121060251 1 21061296 2.51E-11 2.83E-06
vg0225412891 sf0225407022 2 25412891 1.36E-10 8.68E-07
vg0222765370 sf0222759501 2 22765370 4.09E-10 2.91E-06
vg0222673059 sf0222667190 2 22673059 9.19E-10 1.63E-09
vg0401363131 sf0401358681 4 1363131 2.22E-09 NA
vg0224664402 sf0224658533 2 24664402 5.74E-09 4.55E-06
vg0223069005 sf0223063136 2 23069005 1.40E-08 4.03E-07
vg0222857256 sf0222851387 2 22857256 2.93E-08 2.63E-06
vg0221658331 sf0221652462 2 21658331 3.38E-08 4.53E-06
vg0224878279 sf0224872410 2 24878279 3.51E-08 4.03E-06
vg0223720170 sf0223714301 2 23720170 8.91E-08 5.67E-07
vg0319004736 sf0319003496 3 19004736 NA 3.17E-06
vg0622530812 sf0622529815 6 22530812 NA 3.61E-06
vg0209234214 sf0209234212 2 9234214 NA 4.70E-06
vg0402151540 sf0402147135 4 2151540 NA 5.92E-06