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 mr1055 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
vg1215967035 sf1215964331 12 15967035 3.78E-48 2.30E-26
vg1011511779 sf1011440598 10 11511779 2.35E-18 1.75E-07
vg0500829493 sf0500829475 5 829493 3.10E-18 NA
vg1110282765 sf1110277342 11 10282765 2.17E-17 7.45E-07
vg1212873997 sf1212871336 12 12873997 6.39E-17 4.74E-06
vg1218663003 sf1218634438 12 18663003 9.09E-16 1.08E-10
vg1117717695 sf1117251551 11 17717695 2.57E-15 6.78E-07
vg1006587700 sf1006603323 10 6587700 7.86E-14 4.78E-09
vg1011512046 sf1011440865 10 11512046 4.52E-12 3.88E-09
vg1022588644 sf1022517118 10 22588644 1.29E-11 2.60E-11
vg1208048502 sf1208045908 12 8048502 1.47E-10 1.50E-07
vg1215852700 sf1215849996 12 15852700 NA 1.95E-14
vg0901555655 sf0901554655 9 1555655 NA 8.57E-09
vg1213186520 sf1213183858 12 13186520 NA 9.12E-09
vg0408293903 sf0408289177 4 8293903 NA 1.73E-07
vg0623791757 sf0623790760 6 23791757 NA 3.75E-07
vg0715496678 sf0715495685 7 15496678 NA 3.84E-07
vg1121334009 sf1120867886 11 21334009 NA 5.17E-07
vg1009559420 sf1009488241 10 9559420 NA 5.33E-07
vg0820168380 sf0820165667 8 20168380 NA 5.86E-07
vg1206197673 sf1206196564 12 6197673 NA 7.27E-07
vg0824114764 sf0824112050 8 24114764 NA 7.38E-07
vg1216585567 sf1216582860 12 16585567 NA 9.18E-07
vg0816293722 sf0816291008 8 16293722 NA 1.03E-06