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 mr1905 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
vg0921553540 sf0921553059 9 21553540 1.60E-11 9.37E-08
vg1102677343 sf1102673247 11 2677343 1.99E-11 3.29E-07
vg0805959254 sf0805958257 8 5959254 5.22E-11 8.44E-07
vg0606346489 sf0606345490 6 6346489 6.25E-11 2.78E-06
vg1215076732 sf1215074073 12 15076732 1.44E-10 7.84E-06
vg0313058915 sf0313057633 3 13058915 1.50E-10 4.72E-06
vg1213717956 sf1213715294 12 13717956 1.78E-10 8.50E-08
vg0207810055 sf0207810054 2 7810055 3.89E-10 3.81E-07
vg1115925850 sf1115460720 11 15925850 1.14E-09 2.06E-06
vg0122493440 sf0122492395 1 22493440 3.10E-09 3.58E-06
vg0223262220 sf0223256351 2 23262220 8.54E-09 4.39E-07
vg0205684729 sf0205684729 2 5684729 1.18E-07 3.64E-06