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 mr1642 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
vg0434823384 sf0434638275 4 34823384 4.16E-08 NA
vg0332409422 sf0332402294 3 32409422 7.50E-08 NA
vg0434821738 sf0434636629 4 34821738 1.81E-07 NA
vg0904833561 sf0904832561 9 4833561 2.73E-07 1.75E-06
vg0719050750 sf0719049757 7 19050750 1.21E-06 1.58E-06
vg0334748146 sf0334741016 3 34748146 2.56E-06 NA
vg0401881382 sf0401876978 4 1881382 3.28E-06 3.22E-06
vg0335609544 sf0335602413 3 35609544 3.53E-06 NA
vg0912739406 sf0912738405 9 12739406 6.10E-06 NA
vg0114152314 sf0114151288 1 14152314 NA 6.09E-07
vg1101202802 sf1101201803 11 1202802 NA 4.15E-06
vg0721760138 sf0721759145 7 21760138 NA 4.91E-06