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 mr1423 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
vg0216973334 sf0216967464 2 16973334 7.11E-48 3.77E-14
vg0216978595 sf0216972725 2 16978595 1.18E-47 5.93E-15
vg0216804396 sf0216798526 2 16804396 3.66E-38 7.56E-18
vg0128362507 sf0128361463 1 28362507 1.90E-33 NA
vg0402172640 sf0402168235 4 2172640 2.65E-33 NA
vg1009544191 sf1009473012 10 9544191 2.02E-32 NA
vg0216768514 sf0216762644 2 16768514 3.31E-32 5.50E-18
vg0718993498 sf0718992505 7 18993498 NA 4.63E-09
vg0217232931 sf0217227061 2 17232931 NA 2.53E-08
vg0719297973 sf0719296980 7 19297973 NA 5.50E-07
vg0432523372 sf0432338264 4 32523372 NA 6.11E-07
vg0719042389 sf0719041396 7 19042389 NA 1.39E-06
vg1128161380 sf1127638159 11 28161380 NA 2.29E-06
vg0213525745 sf0213525741 2 13525745 NA 2.30E-06
vg0719511488 sf0719510495 7 19511488 NA 2.40E-06
vg0217327456 sf0217321586 2 17327456 NA 2.56E-06
vg0913505389 sf0913504388 9 13505389 NA 3.34E-06