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 mr1720 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
vg0520381631 sf0520319103 5 20381631 2.91E-20 2.28E-06
vg0108450212 sf0108449212 1 8450212 3.51E-19 NA
vg0205768155 sf0205768155 2 5768155 4.81E-19 NA
vg1009602228 sf1009531049 10 9602228 1.08E-18 NA
vg0800848981 sf0800847983 8 848981 1.53E-18 NA
vg0917087568 sf0917086567 9 17087568 7.47E-17 7.16E-09
vg0104593340 sf0104592340 1 4593340 2.05E-14 2.45E-06
vg0817921068 sf0817918355 8 17921068 NA 1.86E-08
vg1204785483 sf1204784468 12 4785483 NA 2.79E-08
vg0134160447 sf0134159403 1 34160447 NA 8.86E-08
vg0134190896 sf0134189852 1 34190896 NA 1.04E-07
vg1204027311 sf1204026299 12 4027311 NA 1.29E-07
vg1204810059 sf1204809044 12 4810059 NA 1.82E-07
vg0804650293 sf0804649296 8 4650293 NA 2.73E-07
vg1123564224 sf1123098094 11 23564224 NA 4.59E-07
vg0718182723 sf0718181730 7 18182723 NA 6.04E-07
vg0519650195 sf0519587679 5 19650195 NA 6.74E-07
vg0724428077 sf0724427083 7 24428077 NA 8.02E-07
vg0729013948 sf0729012956 7 29013948 NA 1.84E-06
vg0602909111 sf0602908112 6 2909111 NA 1.95E-06
vg0519502040 sf0519439524 5 19502040 NA 2.17E-06
vg0608011454 sf0608010455 6 8011454 NA 3.59E-06
vg0415197605 sf0414572263 4 15197605 NA 3.78E-06
vg1204623591 sf1204622579 12 4623591 NA 3.83E-06
vg0804975611 sf0804974614 8 4975611 NA 7.87E-06
vg0720636289 sf0720635296 7 20636289 NA 9.51E-06