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 mr1620 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
vg0719182554 sf0719181561 7 19182554 2.96E-67 1.30E-27
vg0719302947 sf0719301954 7 19302947 8.01E-66 1.59E-29
vg0719051231 sf0719050238 7 19051231 3.74E-58 1.22E-26
vg0705233181 sf0705232182 7 5233181 4.62E-46 NA
vg0917542941 sf0917541940 9 17542941 8.93E-46 NA
vg0708219053 sf0708218058 7 8219053 1.17E-44 NA
vg0305022063 sf0305021065 3 5022063 1.19E-44 NA
vg0719091461 sf0719090468 7 19091461 NA 5.54E-21
vg0719071513 sf0719070520 7 19071513 NA 2.41E-16
vg0719064140 sf0719063147 7 19064140 NA 1.42E-13
vg0719413496 sf0719412503 7 19413496 NA 7.27E-13
vg0718955684 sf0718954691 7 18955684 NA 1.05E-12
vg0719345198 sf0719344205 7 19345198 NA 8.15E-10
vg0719154140 sf0719153147 7 19154140 NA 3.69E-09
vg0719050776 sf0719049783 7 19050776 NA 5.66E-09
vg0719466615 sf0719465622 7 19466615 NA 7.05E-09
vg0329561125 sf0329554165 3 29561125 NA 1.89E-08
vg0718971186 sf0718970193 7 18971186 NA 2.14E-08
vg0314945277 sf0314943924 3 14945277 NA 7.79E-08
vg0719067775 sf0719066782 7 19067775 NA 1.04E-07
vg0421592157 sf0421420207 4 21592157 NA 1.28E-07
vg0719140779 sf0719139786 7 19140779 NA 9.91E-07
vg0720661357 sf0720660364 7 20661357 NA 2.39E-06
vg0718985292 sf0718984299 7 18985292 NA 2.53E-06
vg1002989121 sf1002988098 10 2989121 NA 2.63E-06
vg0216352296 sf0216346426 2 16352296 NA 3.89E-06
vg1005427336 sf1005443873 10 5427336 NA 3.90E-06
vg0719618102 sf0719617109 7 19618102 NA 4.48E-06